I don't really see where you're getting this from. If you want to code your control structures in Perl, in-line Perl systems let you do exactly that. The only popular templating tool that imposes restrictions on your data structure is HTML::Template, and even there I find them pretty easy to work within.

There is definitely room in the world for programmatic generation of HTML. You don't need to drag down templating in order to prove the value of your approach.