Here is an example of what my bookmarks look like given a big job planning out a fair few crafts. I was hoping there might be a way to have an option allowing the bookmarks to ignore the potion effects.

It seems like this functionality was default a while ago and was changed here. If possible, making a toggle so people with permanent effects can not have that chunk forever taken out of the bookmarks panel would be nice.

It already exists: Nei options > inventory > ignore overlap with potion effect HUD.