The odd sound of these sentences is not because of the preposition "to".
The reason they sound strange and not quite idiomatic is because of the verb choice.
The tense is correct, "would have [participle]", but the verb "to go" sounds more idiomatic to me than "to be":
If I had studied well, I would have gone to California.
If I had had the money, I would have gone to the University of Cambridge.
I have a feeling there may be some regional dialects where "been" is OK in this context, but "gone" is correct in standard usage, both in the context of "going to a place" and "going to a University".
So to answer your question, there is nothing wrong with "to" in third conditional sentences if you use "to go", but you are correct that if you are going to use "to be", both sentences sound better with your second choice of preposition:
If I had studied well, I would have been in California.
If I had had the money, I would have been at the University of