It took me a couple of panels to "get" how the enclosure really goes together with the various circuit boards and still remaining logical, but after doing it and seeing the end results, the layout is very logical and works well.
As stated, ditch the plastic enclosures for the circuit boards, like the XSP and XEP and get SWG's. PD9's, if used, work best on the small flat plates and standoffs that are sold separately.
The M1 gets put top center, with the EXP mounted either top right next to the panel or bottom right, the limiting factor being the length of the 232 cable. I've found that you can mount a battery shelf to the mid-right and still fit the smaller boards like the XEP, XSP and retrofit hubs below. I've put the full sized boards to the bottom left of the can, eating up the first row for wiring space, then making harnesses for each plug, so to speak, The only item that would get dicey and is limited by cable length would be a M1RB, since that typically plugs into the J header and is limited by the plug length. In the cases I've had to use them without XOVR's, I've had a second enclosure mounted to the right of the main enclosure via close nipples or short stubs of pipe and passed the cabling through them, negating most issues.
I've always preferred bringing my cables into a panel to the top left where possible, then work left to right in the can, working in "levels" and harnesses, either lacing the bundles or using scrap cable (solid) to bundle cables over ty-raps (take more room). I don't like, wherever possible, splitting a ton of cabling into multiple KO's and sides of a can.
If you use stranded cable, it'll automatically take more space because of the insulation size difference.
Once you get about 4-5 expanders (RB's, XOVR's, XIN's) you should start looking at a second or subpanel anyways, and if you're going to lay boards flat or use those that mount flat (212s' or PD9's) the same holds true. IMHO, for most applications, I've come to the belief that the standard hub for RJ45's makes wiring more complicated, especially for separating out power loads or keypad expansion/outputs, not to mention takes a ton of space to maintain any bend radius within the enclosure.