Yes, you're right. The Polo Museale Fiorentino has decided to sell tickets online in this way, offering other vendors the possibility to sell tickets as well. Even the "official" online site is a third party vendor who won the concession to be the "official" channel for online tickets for a certain amount of years. Every vendor has a number of tickets they can sell for each time slot, and they have to pay the Polo Museale a fixed booking fee regardless. The difference in cost is then the third party vendor's charges for using their system.
Which is the best system to buy tickets on? Well, the answer depends. The
cheapest option is directly through the official site but they
often sell out for specific dates and times. So you can start from there. NOTE that they won't refund ANY part of the cost if you need to change or cancel the tickets, so even if is the cheapest solution, it won't be if you end up having to not use them at all or repurchase tickets for another date or time.
Next option: If they are sold out for a date and time you need, then you SHOULD look at other vendors which are slightly more expensive but might have the same date and time available, so I'd suggest to go through that other vendor. They are all authorized resellers of tickets.... some with better customer service than others.
If you're at this point, I would recommend buying through
http://www.uffizi.org/ since the vendor there does offer the possibility to make changes or cancellations (with a fee, but at least you have the option). You can shop around on other sites, but do make sure to check policies before buying!