80 - 100 switches would be a massive installation...
I'm also using the homerun/star topology, but here's what my thoughts are on the daisy chain method. Some of it might be quite obvious so please forgive.
With a daisy chain there will be many 'field' connections on the polling loop wires so the potential for error and the troubleshooting complexity increases.
You could consider creater a loop out of the daisy chain by having the chain end back where it started. This could save your but in case of a wire break somewhere...but what are the odds of a wire breaking after everything is installed? Also with a loop you wouldnt know when the loop was inact and when not all long as all lights continue to work. To ensure the 'loop' was intact you;d need to disconnect one end periodically to see if everything still works. I'm not sure if it woudl be worth it, but the cost of running the little bit of cat5 from the last unit in the chain back to the beginning can't be that much.
The ??? can be the controller, expansion module or a distro module or a hub. It all depends on what you want and how you configure it.
Do you really expect more than 31 devices per floor in your house? Remember you don't have to count the AUX (what you call 3-way) switches since they are not a 'node' on the communication bus. My 2800sqf 2 story house will only end up with about 18 on the ground floor IF i replace all switches with ALC. Maybe you just have a big house.

If you have a lot of walk in closets and such that you want to use ALC in as well i guess it could add up.
Multiple chains can form a brach. A singel chain does not have to equate to a branch. So if you have them make chains of 10 device or so and homerun the end (or BOTH ENDS) of the chain to your wiring panel then you can switch things around later if you had to. Say your 2nd floor ended up with 20 devices and your ground floor with 40 you would take 1 of the chains from the ground floor, join them with the 2nd floor and you'd need only 2 branches rather than 2 for the ground floor and 1 for the 2nd floor. With the risks for cable breaks associated with daisy chains I'd be leary about having more than 10 devices on a chain anyway.
I believe it doesnt really matter which switch is on which branch or which chain. You'd need to check the documentation but i think the scene switches work across al the branches. So the LV guy could run the daisy chain which ever way works for him (e.g. maybe the living room and master bedroom are above each other and can be a single chain, it doesnt have to be by floor, but for trouble shooting it woudl be pretty convenient.
If you go the 10 device per chain way the ?????? in your diagram could be an enhanced hub so that when you're trouble shooting you can use the dip switches to turn of a full chain. It wouldnt be terrbily efficeint use of the enhanced hubs so you'd only have 3 10 device chains on it and it has many for port than that. You'd be using one enhance hub per 'branch' and the 'chains' would start at the hub. You could use distro modules (cheaper and easier to mount in a structured wiring panel) but you'd loose the dip switch based troublshooting capability.
Consideing the quantity of connection on the hubs and to give you the ability to add some devices later it may be better to limit the number of devices to 7 or so per chain. The problem is how to communicate this with the LV guy since he would need to know where thee AUX (3way) switches woudl be so he doesn't count each switch as a 'node'. The way around this could be for you to do the homework and tell him which switchbox locations should be on which chain. Alternatively (if you have faith in the guy) you coudl explain to him that a multiway switch configuration (i.e. 3/4/5 way) only needs a single node.
In your configuration you'd need a cat5 from each AUX (3way) switch to it's master. This means that besides the 'chain' you'd also have these 'point to point' connections between the AUX switch and it's master dimmer. What is concerning me is that if you have a 3 gang switch box and each switch has related AUX's (possible even more than one) you could end up with LOTS of cat5's at these switchboxes. The LV guy will need to do a very good job labelling stuff and you may have a lot of trouble hiding all this LV wiring since you'd not supposed to stuff it in the box. The 'slot in the druwall above the box' method works well, but if you need to cross conenct and hide 3 switches (3 x 5 LV wires) with possibly 3 to 10 cat5's you'd have a very hard time hiding all this through this slot. This is where the star topology really hellps since you can terminate all this stuff on the distro modules and hubs and iit stays organized.
Imagine a 4 way configuration (3 switches and 1 light). At the 'master' location you will have the 'diasy chain' coming and going. Thats 2 cat5's. Then you will have a cat5 from each of the AUX's. So that's 5 cat5's. That only for one 4 way configuration. I have 3 gang boxes in my house that have 2 3-ways and a 4 -way in them. I would be looking at 10 or cat5'e.
Sorry for the long story, but the more i think about it the happier i am i went with the star topology. For the same 3 gang switch box with 2 3 ways and a 4 way I only have 2 cat5's now ( 3 x 3 LV for AUX comms and 1 x 2 LV for the communication bus, 11 conductors = 2 cat5). If you don't have many multiway situations then it will probabaly work quite well or maybe you need a hybrid solution. For bedrooms for example there will be very few multiway situations, but for hallways there will be.
What is your LV guy's problem with the homerun wiring? If this is what you really want he shoudl give it to you or you need to find a different guy. If you're not confortable with what he's proposing don't let him talk you into it since you'll be living with it for a long time and there's other LV guys out there.
SOOOOO, if you did stay with the daisy chain method and you went the 7 or 10 device per chain method your configuration would be:
- ALC controller (standalone one or ELK special one) - gives 1 branch
- ALC expansion module - gives 3 extra branches
- one distro module, hub or enhanced hub per branch.
From the above i think you can conclude that I wouldnt recommend the daisy chain method, but if you stuck with it then i would have the followig additional suggestions:
- get a very good labellering scheme in place (maybe seperate color cat5 for the 'chains' and the 'point to point' connections.
- have each chain created as a 'loop'
- homerun each end of the loop to your wiring panel.
I would probably then save money by not getting the enhanced hubs but instead get the distro modules and mount all 4 of them together with the controleller and expansion module in a structured wiring pannel. This limits troubleshooting a bit, but at least it's very easy to disconnect each branch (rather than each chain) since the connection from the controller/expansion module to the distro modules is cat5/RJ45 which you can easilly plug/unplug. Carefull with the total cable lenght on each branch though (500'), if you exceed that you may as well put 4 enhanced hubs next to your panel.
I've studied the ALC system quite a bit, but my practical experiene is limited to my own install (11 devices so far with another 20 or so to go). So keep that in mind when considering any advice given. If you decide your route i would definetely sketch up your configuration and run it by TS at SETNET for another check.
Best of luck to you.