Hi Mr. maiki,
Considering your insistence over the years on this specific topic, I'm not really sure if your concerns are genuine or this is just some sort of smart trolling, in which case I'll inform you we've had legendary trolls in this forum, who set the bar really high.
That said, and with regards to the DOS/Linux vs Windows issue, I'll make it clear that I'm from the old-school type too (e.g. check my ATOM-15 bios mode code).
If AdvanceMAME ever recommended Linux over Windows was not due to v-sync accuracy, but to the fact that AdvanceMAME could only program video hardware directly on the Linux OS* (and DOS). GroovyMAME can program video hardware directly on both Linux and Windows platforms (Radeon cards).
I share your concern about running on top of a multitasking non-real-time OS, but you need to understand that on this regard, nowadays Linux is not any better than Windows.
As a matter of fact, actual measurements done by many members of this forum on different hardware systematically show that Linux has terrible input latency as compared to Windows, no matter how optimized the kernel is. Surprised? I was the first one surprised, but these are facts, we do real measurements, we not simply believe whatever ---That which is odiferous and causeth plants to grow--- you find on the web.
As a note, you won't run on kernel mode either on Linux or Windows, unless you are a kernel module such as a driver. Linux is no lower-level than Windows, if you see what I mean.
I'd buy your DOS suggestion, honestly. If I could use DOS I'd be able to add super cool features to GM. But you simply cannot be serious about suggesting DOS in 2017, unless you want to rennounce to basic things like audio, etc.
So, if you want to run emulation on new hardware, you need Windows. I hate Windows too but Linux is not answer. Let be be clear: Linux is super cool for a lot of reasons, but not for the ones you suggest.
Finally, the idea behind GM is that with the proper hardware, you can bypass all the annoyances introduced by multitasking non-real-time operating systems, and achieve perfect timing. You clearly haven't seen it.
* AdvanceMAME had actually a driver for Windows NT but it's functionallity was more limited.