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)?
No, Waymoot would only get 1 VP Tokens placed on it, since it isn't in play.
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, but this only occurs if it is "in play."
Once on page 8 under Start of Round
On the same page under Assign Agent, they define what it means for a building to be in play.
@user1873 Note in the bit you quoted "If any of those Buildings are in play, follow the start-of-round instructions for each." Note also on page 9 under the rules for the Builder's Hall, "Once a new Building is in play, it is available for anyone to assign an Agent to"
Which means that while the building is in the three Builder's Hall spaces it is not in play. Therefore you should not follow the start of round instructions for it, because those are for buildings that are in play. This is why the rules for those buildings specify "when purchased and at start of round", because otherwise they would enter play without any tokens or cubes on them.
Note also that the VP chips placed on buildings in the Builder's Hall at the start of the round are a reward for the person who builds it, while the VP chips placed on the Waymoot are a reward for the person who uses the building. If the building was supposed to be stocked while it was still in the Builder's Hall you would need to maintain two discrete piles of VP chips. Both common sense and the rules say that the "when purchased and at start of round" effects only occur after the point at which the building has been purchased.
Edit: Also note the FAQ here: http://boardgamegeek.com/wiki/page/Lords_of_Waterdeep_FAQ
"Q: With buildings that accumulate resources, such as 'Caravan Court', are resources placed on them while they are unbuilt (still in 'Builder's Hall')?
A: No. Note 1: Those buildings do not have resources placed on them until they are in play."