You are right about how fish are wary works.
I think lowering gathering to catch the fish you want has been debunked. Outside of knowing some fish bite only once a min. has been hit, and so if you can't get those fish, naturally you won't end up wasting casts on them.
In my scenario, it would loot table first. So say there are 3 fish you catch in the area. After the cast it rolls to see which one you've attempted to catch. Your stats would then be vs that fish. That loot table is separate and does not consult your stats, accept to see if you meet the min requirement to catch all the fish on the table.
Like unspoiled nodes vs regular nodes, it seems you can get 100% gathering rate on regular fish, but you can't always catch big fish. So it might cap out at 95%? Though maybe there is just a slippery rating.
This is just guesswork.
