Just wanted to clear a few things up for you. The 3.29% that you were offered for pre-approval was this high simply because it was a pre-approval (unless it is from a bank with high rates, at which point it wouldn't matter). Lenders often charge a premium on pre-approval rates which is why you don't see extremely low rates quoted on a pre-approval basis. You were then quoted 2.99%. The person who quoted you this rate likely quoted it because he/she knew that you actually have an accepted offer, and don't require a pre-approval - you require an actual approval. If they didn't know this then they should have made it clear that it will only become available once a purchase is made. For 'live files,' much cheaper rates are available, like the 2.99% that you were quoted.
If you speak to a broker about rates, they will have different rates available whether you are in the pre-approval stage, or in the actual approval stage - which is what you're seeing, and which is why the discrepancy in rate likely exists. Brokers can not guarantee you the lowest rates in the market until you actually have an accepted offer.
In response to your other inquiry - yes often the lowest rates in the market have a reduction in pre-payment options or more aggressive penalty calculations (slightly restricted products). This is not always the case, though. Also, depending on your goals with the mortgage and the property, the cheaper rate rate may outweigh the negatives of the restrictions. It's different for everyone depending on their preferences.
Concierge Mortgage Group