Note that using DESTDIR is subtly different than using --prefix. E.g., one notable difference is what libtool will set RUNPATH to. I suppose it doesn't matter much for Windows builds though.
I know it's different in general, though I'm not specifically aware of the details with libtool and RUNPATH. My reasoning is that whatever is eventually going to use those libraries is probably going to use neither the default prefix `/usr/local` nor whatever `$PWD/destdir` happens to be, so using `DESTDIR` is not more broken than setting a non-default prefix. Also, I am not aware of any way in which a DLL can meaningfully store a Unix path, so the prefix shouldn't be relevant in any case.