Might as well get a simple trip just to avoid any confusion caused by my dynamic IP.
Alright, I've done quite a few tests, which fortunately proved to be very fruitful. Here's the full story, tl;dr at the bottom.
When I first started playing the PC98 games, DOSBox-X was my emulator of choice, mainly due to its more user friendly interface compared to Project Neko and due to its dynamic recompiler, which seemed to work more efficiently on my weak PC.
After a while, I've learnt about the DWM being a thing, and exclusive fullscreen mode being the only way to avoid it and play with lower input lag. DOSBox-X has no support for exclusive fullscreen (yet, at least), thus I've looked back at Neko Project, and between fmgen and 21/W I went with the one which seemed to be updated more frequently (and had a proper home page). The latest version didn't support exclusive fullscreen though, so I was forced to grab an older version, the latest among the ones which still supported it. In hindsight, I should have taken a second look at fmgen right there, as I've now found out it supports exclusive fullscreen even on its latest version. Also, 21/W seems to crash every time I switch to fullscreen on the newer PC I'm using now, so I can safely scrap it.
NP21fmgen seems to run quite well, although at the default speed multiplier set on the all-in-one pack (x64) it seems to hit some sort of limit even on this Ryzen 3600X, so I've had to bump it down to x54 for it to run smoothly. This brings me to the second matter: emulation speed.
As the guy on the thread you've linked mentions, MS Extra is the most crucial stress test in the whole series, especially this part with the cards all firing huge bullets at the same time:
https://files.catbox.moe/ojs49d.png