The first fix was something I found on Oracle's patchset and allowed me to use the last Flash Player compiled for Solaris, from all the way back in 2012. Still works with most Flash content.
The second is an evolution of what I had to do to get Interlink to compile. For Interlink, I basically had to copy the contents of any boolean values from confvars.sh into the empty moz.configure file, otherwise nothing would get configured. I decided to test whether Pale Moon had the same issue, and it turned out that it wasn't as bad as on Interlink, but it was still pure luck that the browser component built at all, because MOZ_PHOENIX and other important flags were apparently not being defined at all, hence why I couldn't get half the extensions to be compatible at first.
I don't know why this is the case, but apparently configure.in isn't able to import values from confvars.sh. old-configure.in seems immune to the problem that application-specific configure.in files were experiencing, though. confvars.sh itself seems to work fine with values that aren't passed along via configure.in, though. So it's the interface between those two files that is messed up.