You've asked a lot of questions, so I'll stick with those that I feel more confident answering.
If each dice is biased to a different number, can we really talk about a significant loss of randomness in the final result?
I don't think dice bias can cause a significant problem, given that you'll roll it 99 times as said. As I have already demonstrated, even in a
very biased dice which results in '6' half of the time and every other result 10% of the time each, the generated entropy is
more than necessary.
To take this further, how could someone take advantage of the bias in my dice to bruteforce my seed without knowing what that bias is?
It's all about entropy. If a biased dice gives only 1 bit of entropy in every roll, then 99 rolls would give you 99 bits. All the attacker needs to do is brute force anything in the range of 99 bits, because you can't have possibly exceed that. Practically speaking, that could be implemented by a program that hashes sequences of biased results. (i.e., attempt #1: hash("666123"))