A look at the Makefile.PL of Apache::Template shows that all of the configuration options have req_override set to "RSRC_CONF", which forces them to only appear in the main part of the config (or virtual host). So, as written, it look like you're up a creek, yes.
Now, I'm not sure why they made those configuration directives are set up that way (as it seems to contradict the examples). You might try setting some or all of those req_override options to "OR_ALL" (meaning available anywhere). Glancing at the code, it looks like Apache::Template has DIR_MERGE subroutines, so it should work in theory. Re-run the modified Makefile.PL, make< && make test && make install, and give it a try. Let us know what happens. ;>
perl -pe '"I lo*`+$^X$\"$]!$/"=~m%(.*)%s;$_=$1;y^`+*^e v^#$&V"+@( NO CARRIER'