The two seasons before I replaced my tanks I'd done more one engine on low power entrances than I care to remember, I'd cleared most of he bug but had rust coming through too, on the last run out I changed 6 pairs of pre-filters, there's no way I'd have linked tanks.
On my previous boat I'd had both tanks out and cut open to replace rotten steel and got them clean enough to use the house vacuum cleaner inside without violence from swmbo before welding back up, all fuel had been filtered and traeted going back in, I'd only picked up at one marina after that before a sea trip and had fuel issues, found a flake of crud wedged in a pickup pipe that certainly wasn't there before.
We ended up being towed in to kings lynn by skeggy lifeboat as a steering arm snapped on one outdrive, of course it had to be the one still running!!!!!! Could've gone round in circles all day if I'd wanted.
I love seperate tanks.