I would not be a fan of comingling funds. This is a pretty obvious one.
On the subject of completion times and penalties:
I would turn down anyone demanding a guarantee and penalties. There's plenty of things out of the builder's control that can destroy a timeline. The list is endless and in many cases out of the hands of the builder.
If you require promises, let me tell you about a distant acquaintance. His mid size local builder made a lot of promises and commitments to him. They then proceeded to not even complete the rough ins on his home (long distance owner) and drew 100% of the construction funds from him. I saw the home myself and was asked to finish it. The work was trash. I declined the job, as I wasn't comfortable finishing up the poor canvas that he had.
He ended up paying more than 200% of his original price to finish the job. The corrupt builder tried to claim bankruptcy and is under criminal investigation.
But, he did make promises.
My point, good, experienced builders won't make promises they can't keep (or won't die to keep) unless they're a slam dunk or there is a lot of money to be made for doing so. A desperate one will be happy to take a nice deposit and promise you the moon.