I am not a prdigy dealer so am not 100% sure as to how it works but I will give you the answers that I can.
1) For multi-room retro installs with no wire between (individual TV,BD, etc.), in the RTI world, I would install individual XP6, XP8, etc. Is the Crestron way to put multiple PMC2 in each individual room and map each remote to the PMC2 in that room?
I would have to say yes. Ideally you should try to sell the customer on getting wires run as it will eliminate the need for all the processors
2) If this is true, what happens to MobilePro? Can 1 mobilepro install/device control separate rooms? In other words, can they move between rooms, connect to that processor, and use their iDevice?
Not sure with the prodigy composer but Adagio composer you are able to create something called an RSD (Remote System Definition) which allows for each processor to communicate with each other via the network. The more remote processors you have to more programming time you use as you have to connect each RSD file to the "Main" processor (the one that you are attaching MobilePro to). You could also create a MobilePro design for each processor but that will encorporate a lot of port forwarding on the customers network.
3) Does anyone have any leads on custom GUI for the PTX3? The stock really is awful.
Sorry can't help you there. I am sure there are GUIs around that use the same resolution as the PTX3
4) I looked through Prodigy Composer and was surprised by the lack of a good device database. In RTI, we had the mega user databases -- is there an equivalent for Crestron or are we forced to buy the learner?
Again I am not 100% sure but if you have a .CCF editor you are likely to find the codes you need without having to purchase the learner. Since we are a full Crestron dealer I get their full database (not sure if this is true for A**D dealers).