The homebrew launcher is not the only way of starting EmuNAND9, but, yup, that's correct. Somewhat of a chicken egg problem. The main upside with providing your own starter pack would be that you could make sure that the users have the exact right files, in the exact right structure, on their SD cards after running Ninjhax. Slightly unrelated, but also note that you are not forced to run EmuNAND9 from the same SD card that will be set up for EmuNAND.
You also asked if EmuNAND9 asks for more confirmations... I'd advice you to try yourself, but, yes. If the starter.bin is missing, you will be asked if you want to continue. Then you will be asked to confirm that the SD card should be formatted (you can also switch SD cards in that step), this step requires inputting a button sequence (safety first). Then you will be given a summary of the inserted SD card, which you already have to confirm. Afterwards it sets everything up.