mod_perl does not really impose any limits as compared to vanilla Perl - in fact it lets you get up close and personal with Apache if you want.
What you do lose with mod_perl as say compared to vanilla Perl is the ability to write sloppy, poorly structured code. I recommend reading this this from the mod_perl documentation before you read anything else. There are a few traps, some simple and some fascinating/excruciating but you need to use mod_perl to get the same performance as mod_php. http://www.linux.com/feature/55807
