Fin regrowth is first transparent, and the color gradually fills in over time. If the transparent spots are only over where the holes were, I wouldn't worry. If transparency is occuring elsewhere, then hopefully someone else here has an idea as to what's goin on. Just keep an eye on his behavior.
Bettas do fine in soft water. 90% water changes every other day in a 2-gal is good when you're trying to control a disease the fish has because it ensures that the water is pristine (100% changes every day are even better--that way you know nothing is building up). For a healthy fish, that frequency is not really necessary.
Water conditioners usually just break down chlorine and chloramine present in the water, so if you're sure you don't have any of those, a conditioner probably won't make much of a difference. They do sell stress coat conditioners at pet stores, some with aloe vera, which may make a difference. If the betta is acting fine, though, it's probably not vital.