The 'green box' that shows where you should put soil (artificial or overgrowth) gets messed up for the normal Jellynut planters with this mod installed, mainly some spots that work just fine with Overgrowth don't show the green box for you to place it there (i've made sure no trees etc are in the way)

Yeap, this is a side-effect of the soil being okay for the slipstack - so it should show green, because it is a valid place for the slipstack. This is one of the reasons that the Devs went from ~8 harvestable plants, to 2, and made sure they are a long way away from each other. There is no way to override this behaviour, and it is unfortunate that the slipstacks really are at home in the Jellynut biome wetlands.

My brain handles it fine - if i see water, I think doesn't matter if its green or not, Jellynuts need land. And after being exposed to this issue I've gotten use to it. Sorry that there is no fix for this.

Would it be difficult for an Option to NOT modify the Soil 'helper' (green box thing) behavior and just 'figure it out' with the Slipstacks but still have the green boxes for Jellynut?

It is possible, I will look into that in a future update. It tends to not be a problem with all the other farming mods I've got (boompuff, and Stingfrond) because their biomes never overlap. But I can understand how it is confusing for the Slipstacks.

I actually noticed earlier tonight that it ALSO breaks the Green Box thing by making spots that used to not popup for overgrowth due to one of the 9 tiles being invalid now shows a green box if even ONE of the 9 ARE valid, which wouldn't plant a tree anyway, and this happens for both jelly nut and yamako. But I have a feeling it's the same cause of the slipstack soil logic.

Added a setting for this for ya, so you can turn off the Jellynut placement UI if you wish!

Thank you so much! I know this is all done in your spare time, and I am very grateful! I will never demand things from people who give freely! Thank you again!

No worries mate, I've been enjoying making mods that others are enjoying to use!