It apparently added a Modules section with a Load "glx" command but why
would that stop the extmod extension from auto-loading?
Because your modules section looked like:
Section "Modules"
Load "glx"
EndSection
If it were empty, or nonexistant, then we'd load the default set, which
includes glx. But since it has exactly one entry, we load just the
modules you ask for, and nothing else.
Hence "added a Modules section that it didn't need to". GLX is in the
default module set! The driver install script needs to not muck with
the Modules section, period. You know, the same way none of the drivers
in core touch xorg.conf.