I am running the TWilight Menu via SCFG access on a R4i Gold 3DS Plus in a new 2DS XL and after fiddling around like the dumbass I am, I managed to find out the following.
First, my initial thought, that Red Riding Hood Zombie BBQ and Metalsug 7 would benefit from TWL clock speed and VRAM boost proofed to be correct. The slowdowns are gone (or at least for me no longer noticeable).
Second, there is a soft rest option (L+R+Down+A+B... I think?) which does kinda work, only that I end up on the TWilight Menu that runs on the R4 (as if I had started the card via the TWL Slot 1 Launcher. I am running this
https://gbatemp.net/download/luma-10-2-1-with-redshift-and-quick-switchers.35619/ Luma build and needed a way to start my card before I switched to Twilight Menu)
Third, booting DSi enhanced games in DSI mode just doesn't work... DSiWare however does work for the most part (I had to turn off the option to temporarily copy the DSiWare to the console's DS card, that just didn't work for me at all.)
Fourth, cheat function is only available when running bootstrap, when booting via the flashcard kernel cheats are just not available, which is a little bit sad face but all in all a trade-off I can live with.
Fifth, while this Homebrew (at least the way I am running it) is far from intuitive, it is nonetheless a tremendous achievement. Having basically a second SD card slot dedicated to DS games on my 2DS is a godsend!
Anyway... sorry for all my rambling, and thank you for this awesome piece of Homebrew. I do hope you continue on improving it in the future.