Caveat lector: I don’t know what I’m talking about, because I haven’t written any code that embeds a Perl interpreter.

That said, if the embedding interface works the way I would intuitively expect it from my experience with the way things work when writing Perl that runs in a standalone interpreter then global variables are initialised when the code that initialises them runs, which is usually part of the file-level code, so that would be when you call perl_run; however, if the initialisation is within BEGIN blocks or such, it will happen when you call perl_parse.

And if mod_perl is any indication, then global variables are retained between function calls.

Makeshifts last the longest.