Renaming the file (with a space in its name) isn't an option for me.

Well then, I guess making your package easy to port across platforms won't be an option either...

I don't know where the file names are coming from (a pipeline? a list file? File::Find or readdir running inside ExtUtils::Manifest?). If you have a chance to manipulate the list of file names before passing it to ExtUtils::Manifest, you might try converting space to something else (just within the list, without actually changing the directory entry for the file), then undo the conversion (turn it back into space) after ExtUtils::Manifest is done with it.

(... Just guessing.)