Thanks Alex, you've pretty much answered all my questions. I have a bit of confusion though, because for me, [declare] in 0.48 does seem to add custom search paths (see attached screenshot). Doesn't this contradict what you said?
As to whether I should do it or not, I have users telling me that I should and developers telling me that I shouldn't, which puts me in a bit of a bind. Ultimately, I'm worried that a complex install process will scare a lot of new users off, which is why I'm looking for a solution. I've given up on many computer programs before simply because I couldn't get them to work in the first 5 minutes; haven't you?