I haven't used any of these modules either, but based on the evidence you've shown, it seems like the "legacy" behavior of "Locale::Maketext::Extract / xgettext.pl" is sub-optimal (to put it nicely) because it is non-compliant with the other tools that it is supposed to interact with.

So, speaking as an outsider, my vote would be to change the default behavior so as to make it "correct" (compliant with gettext and POEdit), but keep the legacy behavior as an option (in case anyone has actually created code dependent on that format), and be very clear about the change in the docs. (And mention that this "backward compatible" option will be deprecated.)

Among the people who have used Local::Maketext::Extract / xgettext.pl, I wonder how many of them have considered its original output format to be troublesome because of its divergence from the norm? (For that matter, I wonder if this issue was involved in one of the POEdit change-log entries:

Version 1.3.5
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- fixed crash when loading some invalid PO files (#1495970)
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