The key to keeping gear sets manageable is to take levels into consideration. Aside from their main and offhand tools, each crafting class can use the same gear in each slot - and each gathering class can as well. So if you level 7 crafts up to 15 for extra skills, thats only one set of "wearable" gear with 7 different tool sets, then CUL would have its own leveled up set, and you could get BOT/MIN/FSH to share as well if you level them at roughly the same speed.

As for scrip gathering, i wouldnt worry about it. You can get them with any gathering class and spend them as you see fit. So using miner to collect then spending on fisher supplies(as an example) is perfectly viable. The reason that bot/min are usually paired separately from fsh is that fishing has a large amount of rng in getting what you want. Miner/botanist can walk up to a node and know what theyre getting and how much/how quickly. A fisher walks up to a body of water(etc), picks a bait, casts and hopes for the best. Whether thats a feature of the system or a reason to hate it is up to personal considerations.