Having (at least) a option that allows HBL to read/recognize DS(i) carts where we can extract/inject save files/roms is pretty much a big step and is a step towards what a lot of people want, going so far and adding it to where you can run it in regionfree is something else that i wouldn't be completely expect. Personally, if it ever came to it, i myself would only prefer to be able to extract/inject save files into my retail DS cartridge, i have no problems running it strictly from the 3ds OS just as long as i could make tweaks to my saves whenever i'd like through HBL.
I was talking with someone about this and they had told me that they'd have to write a TWL_FIRM specifically to recognize/run retail DS cartridges, but wasn't sure if it was something strictly from DSi eShop versions or both DS(i) eShop and retail carts.
Imo, i don't think it's as hard as people make it seem. It's just people haven't looked into coding it as extensively as the people who request this would like.