I boot ROMs that I've put in the saves folder via flashcard's menu, and I boot ROMs I've put in the folder before saves with TM++, doubles the size taken by ROMs, but works as intended without creating separate folders thankfully. The only downsides are aforementioned doubled capacity needed and...
In my particular example, the Flashcard in use is r4isdhc.hk 2023 that runs Ace3DS+ R4iLS Wood R4 1.62, from which I manually boot up Twilight Menu when I need nds-bootstrap.
Since Twilight Menu uses a dedicated 'saves' folder (Let's assume I keep all my ROMs in one folder, so the 'saves' one...
The worst is when its a dry poop, then you spend 20 minutes and ha!f a roll of TP wiping. Its like wiping TP over a magic marker, just won't stop showing.