From what I understand as regards online Florence museum tickets is that each site - even the official one - only has a certain number of spaces allotted to them. So while one site might show that there are no more tickets for a day or time, another site might still offer them.
Even if you were to find everything booked, it only means that the spaces which were sold for advanced booking are taken -- you can always go and stand in line to get in. There might be a wait, but you will get in eventually.
Unfortunately, you have no choice on whether to see the temporary exhibition or not - when there is one going on, you have to pay the additional $ for that.
As for sites that sell museum tickets - after studying various of them, we decided to partner with
Florence Tickets which is specialized in Florence museum tickets. Our experience with them has shown them to be professional and trustworthy despite the additional booking fee. You can reach their site by clicking on the banner found at the bottom of this thread and in this way support our site as well!