I agree with your speculation about the boots. Western boots are expensive due to being well-made and durable; if the killer or accomplice was wearing crappy too-small shoes that had been oddly repaired, he or an accomplice well could've been tempted to take the boots off the UID's feet (which were probably at least a size 12, so would have fit better than a too-small pair of sneakers). Of course, I like boots too, being a SW gal, so I'm also biased.
One minor aside -
pretty sure it was the waistband (with the size written on it) that had survived the elements, and the rest of the underwear had disintegrated.