h2ph is passe and it became passe because it had problems. I suspect that your /usr/include/stdarg.h contains:
#define __need__va_list 1 /*or something*/
and h2ph just translates it into some Perl approximation of the same thing and does it in a way that isn't clean when warnings are enabled (perhaps that warning was added after h2ph stopped being actively maintained).
It would probably be pretty easy for you as a human (and thus being much smarter than the h2ph script) to clean up stdarg.ph to make it not emit any warnings. Avoiding new uses of h2ph and *.ph files would also be a good idea, BTW (though I'm not implying any judgement on what you are currently doing).
(but my friends call me "Tye")
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