A slightly thicker MCPCB shouldn’t be necessary, but should work just fine. The pill will screw in just a little bit less than usual, resulting in a tiny gap between the head and tail sections (additional gap equal to the extra height of the new MCPCB).

You’re right about those LEDs, they sound work fine. Some others, such as the XP-L, have a larger dome and likely won’t nest into the optic properly without drilling it out (not something I’d really recommend unless you had to).