Well, I looked through the old code (manually, like an archeologist), and it goes way, way, way back to version 1.2 (6 years, 4 months ago):
http://cvs.apache.org/viewcvs.cgi/modperl/Makefile.PL?r1=1.2&r2=1.3&diff_format=h
First seen here on line 294 as: $EXTRA_CFLAGS .= join(" ", split(",", " $PERL_EXTRA_CFLAGS")) if $PERL_EXTRA_CFLAGS;
A subsequent checkin, 1.4, changes it to the form we see today. It was the first revision to actually set $PERL_EXTRA_CFLAGS to something, apparently relating to expiremental features. Revision 1.144 just moves that block around.
Unfortunately I couldn't find any mailing list traffic for January, 1998, and the log messages aren't terribly helpful either.
The problem is that as of 1.160, $PERL_EXTRA_CFLAGS gets set to include $Config::Config{ccflags}, which may contain all sorts of crazy strings that wasn't taken into account at 1.2.
As to the question about the flag causing this mess, "-Wa,xarch=v9", I don't think it's an absolute requirement for 64-bit, but I believe it's added for you if you build perl on solaris sparcv9 64-bit.
I think it's reasonable that we remove that code. And if that breaks something we will fix it and document why we did that. I've committed that removal change.
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