Compatibility info for Linux and Mac users: I've just finished replaying all of the games on Linux. I mostly used the HD versions that I purchased a decade ago, but I realised that although I definitely bought Submachine 10 I didn't have a copy of the SWF anywhere (although I did have the free web version), so I repurchased the latest EXE version of that specific game. I was able to extract the SWF without any issues using the Python script linked from this page.
I assume that the collection is still fully playable in the standalone flash player, although I have not tested this directly with these new builds (unfortunately I'd already played through my old copies of 1-9 when I found this page). These games have brought me a lot of joy over the years, so I will probably buy this collection soon and replay them again, using all of the new builds, and report back.
I was able to play through most of the collection using the latest version of Ruffle, with some exceptions:
1. Submachine 10 struggled visibly in some graphics-heavy sections and eventually crashed when I played it on a laptop with 8G of RAM (and Firefox open!). I then moved to a laptop with a lot more memory available, and it was fine, except...
2. Submachine 10 consistently crashed towards the end of the game when I clicked on a specific portal. I don't know if this is an issue with this specific version of Ruffle, or this new build of Submachine 10, or my specific graphics hardware or software. I was able to copy the save file from just before the crash from Ruffle to Flash, play that short section in the standalone flash player that I still have, then copy the save file back and play the rest of the game in Ruffle.
WARNING: the game only saves progress (in Ruffle) if you exit the program normally. If you play the whole game without saving and it crashes, you will lose all of your progress. I did this twice, because I don't learn from my mistakes, and then started quitting periodically to save.
3. 32 Chambers has a glitch in Ruffle which breaks the game. I played this whole game in the standalone flash player.
It's worth noting that Ruffle is an actively developed project with multiple contributors. While I was looking into these issues, I found a lot of reports of previous problems in the Submachine games which have since been resolved -- so these outstanding issues may also be fixed soon.