I have fairly pronounced trypophobia too. I was under the impression that the leading theory is an evolutionary one; that certain burrowing insects will lay eggs in the skin causing a pattern of holes and that our brains have been trained to read this and other parasites. Yours is certainly interesting, though anecdotally I can look at a very regular pattern of holes and not feel the effect. It only really "bugs" me with more irregular, organic patterns.
I get a mild disgust/nausea/skin-crawl reaction. I lean towards evolutionary theory: your lizard brain is telling you "don't touch/eat this parasite-infested item". The worst trigger for me was an image was a (photoshopped) picture of skin with holes, and some had maggots in them.
