My understanding (and I could be wrong) is that PolyMega licensed a couple of the same "emulation-cores" that are used in Mednafen, such as Rypheca's personally-written Saturn emulation (which she is free to license however she wishes).
The resulting PolyMega Saturn emulation will undoubtedly contain some PolyMega-proprietary interfaces and code that will never be ported back to Mednafen ... but it seems unbelievably unlikely that any of the actually-important bug fixes in the shared-core of the Saturn emulation won't make it back into Mednafen. There is just no reason to believe that Rypheca would ever agree to terms like those. She has the power in this business relationship-of-convenience, and PolyMega needs her Saturn emulator (to provide a selling-point for their silly console) far more than she needs their money and promises. She has put too much work into creating Mednafen for her to hamstring it in order to appease this team of barely-competent would-be-entrepreneurs.
I think that the best indication of whether there is continuing improvement in Mednafen's Saturn emulation, is to just look at the bug log on Mednafen's forum.
Sorry, but you can't just argue both sides of the argument in that way. How can someone "just get the version that works best" and simultaneously "don't care about versions and this and that and who's using what emulator"?
If you're going to use an emulator, then it is important to know which basic emulator you're using ... their quality-level, bugs and support are not identical, especially when it comes to "cutting-edge" emulation like the Saturn. That is not because the Saturn is an amazingly-powerful machine, it's more because the Saturn is a terrible design of multiple thrown-together bits of hardware with lots of undocumented and unpredictable interactions with each-other, that various games relied upon either explicitly, or by accident (i.e. a bug).
It's the same with FPGA cores ... sure, they offer the prospect of much more faithful recreations of the actual processing in the original consoles, together with low-power usage, but an FPGA-based recreation isn't magic, it is still a piece of software that is the product of a person/team of humans.
I personally trust the quality of kevtris's work and his fanatical attention-to-detail, far more than I trust the people who are developing the MiST/MiSTer cores.
In the same way, I trust Mednafen's software-emulation of some of its supported consoles (but not all), more than I trust other projects.