That comment is about why the ctrlr files (usually*) doesn't work*, and it's not unchangeable as "hardcoded" usually implies. They are remapped in the source code (aka "hardcoded"), but can be changed in mame's UI menu just like normal. However, since the source mapping (usually*) overrides ctrlr mapping, it feels hardcoded.*
It looks like mame still remaps in source spyhunter's shift (to enter, though), and outrun (to space).
Maybe the comments should be clarified, but not removed IMO.
*BTW, you can get the ctrlr file to work. Remap the remaped in source input back to "default" by using the tab, "Input (this game)" remap, but do enter, esc, wait until mame shows "none", enter, esc, wait until mame shows the normal default. The ctrlr file remaps work only if the input is mapped to "default" in the "Input (this game)" menu. It's a pain, and the ctrlr file in general is there so you don't have to edit by hand the inputs through the tab menu, true, but it's possible.