Yes, in theory you can swap those files. You just need to make sure they are both correctly formatted and that they contain the same 'naming' : that eg. gene_id is consistently used to denote the genes (and thus not gene_id in file A and parent_id in file B), or adapt your htseq count cmd accordingly.

Those two file types are nothing specifically for splice sites and/or names. They are simply alternatives from each other, they both contain gene annotations in their respected format