IOW did you have an associated DOS window or did you use wperl?
They are usual cmd.exe console window and perl.exe interpreter. Actually, GUI warnings for CLI tools was long standing issue for libtiff and Windows, e.g. link. Some defines were messed-up in C source, IIRC.
However, I'm glad to stand corrected: as I'm checking now, in Strawberry Perl 220.127.116.11 (libtiff 4.0.7), there are "ugly GUI pop-ups" for warnings with libtiff, but in 18.104.22.168 (libtiff 4.0.10) there are "proper and nice" console messages. They finally fixed it, but not very long ago.
consider sending a patch request to the module's maintainer
when/if I have patch-quality solution, not proof-of-concept/cuff-scribbles code:) If only for a reason, that Inline::C should probably be converted to XS (which I have no experience with) to match Graphics::TIFF source