I first noticed it for some show at the Hudson (maybe Plaza Suite). The ticket price on the Today Tix and Hudson sites was similar, but the fees were different.
I haven't noticed them being more expensive than regular sites.
It seems like there are less promo codes available and more shows on Today Tix. Not a fan of not knowing where I'm sitting, so not a fan of this change.
However, I've also noticed that more offers on Today Tix let you choose your seat. (And I won't buy the ones that don't let you choose.)