The firmware doesn't care what the file extension is. DWC does care to some extent, for example when presenting you with a file upload dialogue.
The "%" character is mentioned in the NIST GCode standard:
"The RS274/NGC language has no indicator for the start of a program. The Interpreter, however,
deals with files. A single program may be in a single file, or a program may be spread across
several files. A file may demarcated with percents in the following way. The first non-blank line of
a file may contain nothing but a percent sign, “%”, possibly surrounded by white space, and later
in the file (normally at the end of the file) there may be a similar line. Demarcating a file with
percents is optional if the file has an M2 or M30 in it, but is required if not. An error will be
signalled if a file has a percent line at the beginning but not at the end. The useful contents of a file
demarcated by percents stop after the second percent line. Anything after that is ignored."
I may change RRF to recognise these %-lines.