How to mark spot as harvested/cleaned/removed/solved in analyzer

After reading through the comments in the reddit post you included it seems that the upgrades do not need to be adjacent to the base function to work. Try to group upgrades together and group with main feature for added bonuses. I'm trying to figure this all out just like everyone else but this has seemed to work for me.

Each additional slot increases the cost by a factor. I don't have exact values. It may be similar to the exosuit upgrades, in which you pay 10k for the first, 10k * 2 for the second, 10k * 3 for the third, etc. Obviously ships have higher cost per slot, but the idea is that it scales as the slots increase. It's not mathematically exponential, but it gets pricey quite fast.

This applies to the baseline, non-upgraded, per-slot cost. As MageXy commented, the value of any upgrades is also added to the price. I've seen identical ships with the same slot count but different upgrades sell for different prices. At 25 slots, two ships differed by at least a million credits, so upgrades can make quite a difference. I'd prefer a non-upgraded ship most of the time anyway, as found/bought ships tend to be a mess in terms of component linking. YMMV.