Is there a difference between using PerlModule Apache::DBI within httpd.conf and using use DBI; within startup.pl (run as PerlRequire "C:/Apache2/conf/startup.pl" within perl.conf)?

There should be. According to the docs of Apache::DBI, the latter serves to create a pool of permanent database connections, which means it changes the behaviour of DBI. OTOH, when just using DBI, without Apache::DBI, you still create a new connection every time a script runs — even though the module itself remains loaded.