I tested NTR Launcher 1.9.5 when I was working on trying to get TWL carts to load before, and with System FLAW (DSi-exclusive) it did manage to boot the ARM9/ARM7 binaries. (It gave me a "This game is for DSi only" screen.) I don't have any other DSi-enhanced or DSi-exclusive cartridges on hand at the moment, though.
EDIT: Maybe Slot-1 reset is needed in order to get back to NTR mode for the cartridge. (command 0x3C)
EDIT 2: I'll take a look at nds-hb-menu's changes for devkitARM r46 and see if I can apply them to NTR Launcher. (...and then synchronize TWLoader's version)