Even some of the clone boards have "3dr" printed on them(I have one), irrespective of that, if the FC works great in the first attempt there is nothing much to worry about unless you goof up somewhere. 3dr carries out quality checks and provides good after sales service, which may not be available with some of the clone suppliers. Other than that its pretty much the same.

3DR provides a 2.6 FC with the onboard magnetometer removed from APM 2.5, where it becomes compulsory to use external magnetometer. While 2.6 clones are nothing but the APM 2.5 with an option to cut tracks to onboard sensor and use an external sensor instead. So we can say that 3DR APM 2.6 was rather a degrade than an upgrade but thats my opinion because we can use external sensor on 2.5 too.

Anyhow since the seller has offered to take it back, it shouldn't be much of a issue. Also Joe be careful while connecting up everything as its very easy to short or reverse polarity on FC's. There is lot of data and info available online in case you get confused.