At the start of the first round, if The Waymoot is one of three starting buildings, do you put 4 VP on it (i.e. 3 from the building description and 1 from the VP on the 1st round area)?
Yes, Waymoot would get 4 VP Tokens placed on it.
The Builder's Hall (page 12) of the rules tells you to take the 3 VP Tokens for the round, and distribute one to each building tile for purchase. The Waymoot has special rules text that takes effect at the When Purchased/Start of Round:
Twice in the rules, they remind you to perform the Builder's Hall Victory Point distribution, and any special building tiles with instructions for the Start of Round. Once on page 8 under Start of Round
and again in the Rules Reference in the Sequence of Play section.