Yes it will work with a rom on Sky3DS.
https://gbatemp.net/threads/pasta-c...d-on-old-and-new-3ds-required-ninjhax.388925/
The rom menu won't open (the menu where you select a game from). This is because the home menu was updated, and breaks Gateway's mapping of the select button. Gateway can fix this with ease though, so you probably won't have to wait long for GW to release an update that fixes it.
Have you unlinked sysNAND and emuNAND? If not I'd recommend doing so. Remove the SD card from your 3DS (this is very important! If you don't remove it, everything on your SD will be deleted!) and format sysNAND. The 3DS will ask you to connect to the internet, but you will not have to update. Now the two should be unlinked and I think this will solve your icon issue.