1. "zone001" refers to the zone number in the M1. I don't think a name would work, but I haven't tried it. The "x1" refers to the device code (aka address or housecode/unitcode) within HomeSeer. For example, my ini file has zone001 to zone032 mapped to x1 to x32 so I have 32 lines in that section.
2. the "zs" update command should put a line in your HomeSeer log for each zone. for example, I get 32 lines of updates. They just show up as the usual info "exec command:...". If your HS devices were already correct, then no, you would not see anything change in an HS status or device list. If a few zones had changed, then yes, you would see them get updated, but that is pretty subtle.
3. No, there is no important output from opening the serial port. Whenever I open the serial port, I immediately do a "zs" to refresh.
The script works great, don't be afraid to ask any more questions. Just don't forget to disconnect from RP or the script is unable to run. (been there, done that)