[MGlitch]

You haven't missed anything, that's the way the mod works.

You could try something like 1% which would still be fairly easy to reach since you're using the nightmode mod you should be able to adjust the brightness percentage in 1% increments. So slide it to 0% then tap to 1%, wait, and then adjust up to what you find comfortable after nightmode is activated.

Editing to clarify

The mod works by allowing the switch to happen after 4 seconds of the brightness control being set to a certain level. You do not need to actually have your finger on the slider for those 4 seconds. It may be possible to require you have your finger on the slider, the Kobo certainly understands short press versus long press. Even with that it may not be possible, I'm not sure of the limits of where the Kobo looks for short or long press, or if it just always does so. This would require changes to the mod, which I do not know how to implement. But perhaps the creator of it could help you.