Never mind, I figured it out:

If .p2k.cfg only partially works on C64: Maybe parts of it get overridden by the C64 emulator settings. To check (On a GPi case):

1. Select B to open Quick Menu
2. Options (select with B)
3. Retropad Mapping Options
4. Remove conflicting entries (set to ---)
5. back → back to Quick Menu
6. Overrides
7. Save Game Overrides

I would like to remap most buttons for the C64 game space crusade, but some don't work (most do).

I'm using Recalbox on a GPi case (Game Boy case, no keyboard).

My .p2k.cfg:

# cat "Space Crusade.d64.p2k.cfg" 
# Toggle scroll
# Does not work, a moves the cursor up (could be a keyboard key)
0:a = s ;; Scroll Mode
# b should be fire, but it's also up?
# ideally, a would be joystick fire and b would be keyboard s

# quick select marine or commander (broken, X does not work)
0:start = 1 ;; Select Commander
0:y = 2 ;; Select Marine 2
# Does not work, x is fixed to space
0:x = 3 ;; Select Marine 3
0:l1 = 4 ;; Select Marine 4
0:r1 = 5 ;; Select Marine 5

It's great that Select brings up an on-screen keyboard, but X being hardwired to Space and Joystick Fire is useless, since this game does not use the space bar.

How can I remap these buttons? Is there some C64 specific config that currently blocks them?