I noticed that wordpress’ make_clickable filter was attached to the comment_text filter hook and not get_comment_text, which is what I have been using for a while. I had researched earlier if this may be the case, specifically figuring out what the difference was between the two, and I think I read something about comment_text using get_comment_text, so maybe it was doing something more than once, resulting in the weird output I found.
I solved this by changing my filter to hook onto comment_text instead, that way the priority would matter (duh), and kept my filter’s priority level of 9000. Preliminary tests show everything to be working. This way I don’t have to worry about wordpress modifying my output in unpredictable ways, instead I can just bother working with what wordpress vomits out. At least that way I know what I can work with and what I can’t work with.
Thanks again to one trick pony for giving me a lead.