Understand the =begin =end =for and friend, just seems like using the L<> would be a little cleaner. For example, I could put the link inline of the paragraph I'm writing in, without having a new paragraph and it would work, wherever you're viewing the POD.
Pity I can't just say in L<>, "hey this is a relative URL, and it doesn't have to turn into anything - just trust me". Seems like that's within Perl culture of Do What I Mean.
I usually make two sets of docs - one that comes with the distribution, and anything that goes on the support site.