Depending on how you want to use the controller you could use one or the other. The APC40B template is setup to use a combination of the Mainplayback Buttons, Faders, various Function Keys, and a few other functions. The Matrix template uses a separate program called Bomes Midi Translator and *.bmtp file to map the grid of buttons to 7 pages of playback buttons and 1 layer of programmer keys. Personally, I don't think the Matrix template and adding a 2nd third party application is adding another layer of complexity to the equation. It may be easier in the beginning to figure out how you want to use your controller and set it up according to your needs.
Most of the controllers that you'll find from AKAI and Novation were designed to operate with Ableton Live. The default mode "0" on the APC40 is setup to use the transport controls, scene launch, volume, pan, etc....Functions which have no practical use in MPC. Mode "1" & "2" are practically no different in regards to functionality. I don't believe the program linked in the first thread for the APC will change the mode on the MK2, but it doesn't hurt to try.
The layout is similar but different, it may be easiest to just start fresh. Use the existing template as a guideline for how each of the functions are programmed, and modify for your style.
The Custom Midi Feedback does rely on feedback from MPC for only a small fraction of the functions. The only functions that send feedback are the MainPlayback Fader, MainPlayback Buttons, Programmer Keys, F-keys. If you want to program a button for a Playback Button, you can still make the button light up on the controller, but it wouldn't recieve On/Off feedback from MPC.