Regarding making the potion be permanent and thus all subsequent potions at risk for miscibility as balancing factor: If this only applies for super-powerful potions like these two, this seems reasonable. It seems a little too much of a downside for having the good fortune of rolling 00 on miscibility if your two potions were Climbing and Animal Friendship, and I would want a consistent ruling that covers both situations.
When it comes to balance, it's worth mentioning that it's not really different from misjudging an encounter and having the big-bad lose their Girdle of Giant Strength to the players or similar. What would you do in that situation?
Not really. 'Have to decide' vs. 'have clear cut rules, but they might be bad' is the same both-could-have-consequences situation as anytime else. Without looking, I have no faith that 3.Xe's rulings on this situation would actually be good.