If I use the transitional DOCTYPE <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/strict.dtd">
but use HTML5 markup on my page, will I incur any deleterious side effects, other than receiving validation errors?
As far as I'm aware, no. Browsers these days just check for the presence of A doctype, not which one. But it could be that I'm missing something - why don't you just try and see?