The FT-60 and the flow scan are compatible with Dynon Skyview.
I believe they have the two models to let people chose the one they think the most reliable and/or the most accurate.
To have any other informations concerning the Skyview system, you can also download the Skyview installation guide on the Dynon website. It is very complete and will help you a lot in understanding how it is wired.
I don't think it is about choice, Vans sent me the one THEY picked out, with no option of choosing one or the other. Not knowing beans about either of them, it would have been an uninformed decision anyway.
Dynon does not sell FloScan with their systems anymore. In fact, other than EBay, I think MGL is the only place you can get one. I know all this because mine died after 300 hours. I performed all the CPR I was aware of and eventually just turned it off. It has a small ferris wheel inside that apparently doesn't rotate anymore or the pick-up light is a goner. All the same, the cheapest available is $200 and its not worth that for something we flew for years without. Lot of money for a gimmick.