Have been doing some additional research and this is what i came up with. The two active enzymes in the protein rest are peptidase and protease. Protease is responsible for the break down of large proteins that cause haze and reduce head retention. In modified malts (which is most malts), these large proteins are ALREADY broken down in the malting process into smaller amino acid chains which aid in head retention and body. The peptidase will break these guys down further into nutes for your yeast. So in short....you end up losing beneficial proteins when you do a protein rest on modified malts, but get healthier yeast...i guess
http://www.winning-homebrew.com/enzymes.html
Of course...there are so many factors in brewing that it might take a professional to notice the difference. But hey...the science is there. Only real way to know is to brew the same beer twice, one with a protein rest and one without, and do a side by side comparison. I dunno if i care enough to do that haha...
Thanks for that. I hadn't had a chance to get back to this yet. In addition ti the science, I'll offer as evidence the beers I've ruined by doing a 122 protein rest with highly modified malts. And it's pretty darn difficult to find any other kind!