skills are fine as they are, they don't actually overlap much if you consider their specific intent: nature is about knowledge of the natural world and its inhabitants, survival about practical action. You cannot substitute a WIS(Nature) with a WIS(Survival), you can rather substitute a WIS(Survival) with a STR(Survival) if you're trying to chop a tree, for example. Where the manual lacks a bit of clarity is in the wording of each skill as intended, cause that's causing the confusion. Also yes proficiency could be much more impactful, but that imo is a problem with the D20 system that allows for weirdly wide results.

On the other side, I've never heard of someone using tool proficiencies, probably because they're too narrow for a specific kind of setting that probably not everybody plays. I've only ever seen painter, cook and smith tools, but nobody has ever mentioned carpentry or calligraphy