Hello Robert,
1. and 2. Cakewalk mimic original analog consoles. I am not sure what you mean by "Groups", but Main is Main and Aux is Bus in Cakewalk. For controlling purpose, you need "Mixer main" bus to which all controlling tracks are pointing (since you want control it separately from Cakewalk "Main", that will influence the volume from Cakewalk). And additional buses "Aux 1", "Aux 2", etc. Each controlling track will have 4 sends to this auxes. Each such send has all parameters (on/off, volume, pan, pre/post), so I guess that is more then sufficient for controlling mixer routing.
In case by "Groups" you mean something like extra Auxes, that can be done the same way as with Auxes. Just note that initialization should set all parameters, remember throughput and processing speed comment (you can overseen the issue testing just one channel, I recommend testing with complete AZ Controller preset for final number of channels even when testing smaller number of physical channels). Otherwise the solution can be like for 3.
3. See my previous comment about FX Chains. You can define "dummy FX chain" with parameters like "Bypass insert", "Group X", etc. and map corresponding values to the mixer. You can not put extra controls on the channel strip or in the track view (unlike in REAPER...) and you can not use ProChannel for that (too buggy design in control surfaces API), so you will need to open "FX GUI" to set/change these parameters. That is a bit less convenient then "Bypass FX" button, but I think still more usable than related procedure on some real DMs (first select the channel, then special parameter page, then parameter...).
Cheers,
Alexey.