You don't really
ever know where the "standard" Perl module directory is, do you? I can override any paths using configure. I can have multiple directories included for past point releases. I can have vendor lib directories (which are used by many Linux distributions (because the distribution is packaged to be reliable across many installations for many users, and many distributions use all sorts of Perl in their distributions-specific tools (like urpmi on Mandriva))).
Given those caveats, if you can get your code to be more reliable rather than less reliable by doctoring your lib paths and you don't intend to mess with the defaults for other programs, then I think every option is open to you.
I'll give you a bit of free advice about common wisdom that not enough people seem to grasp. There are conventions, best practices, and recommendations enough that work well enough for most people in most situations. Usually, it's a good idea to follow the collective wisdom of a well-experienced, thoughtful group. When all the cards are down, so to speak, your chips depend on having the best hand at the table and not a pretty good one on average. If you're finding that you have an odd requirement that falls outside of the common wisdom, then perhaps you're right to have an odd solution. You'd just better be right about it, or someone's going to call you a fool when your system falls down and you have to explain why you stepped outside the norm. If you can make your system ten times as reliable by breaking convention, then do it and document the decision process. If you're making it 100% harder for another Perl programmer to take over the project later for a 5% increase in reliability under someone who knows the whole custom installation and configuration process, you'll be canned and for good reason.