Back then you just used one wallet.dat. I don't see why you would different wallets when you can just create different addresses.
It's for convenience. Of course you can manually separate all your inputs and always use coin control, but that means you're one slip-up away from compromising your privacy on-chain.
The problem is, if you simply move 0.1 BTC from an address with 1000 BTC in order to have this 0.1 BTC to spend from
If you own 1000 BTC in a single address, and that's the only input you own, then indeed, it's going to be difficult to spend part of it without compromising your privacy. But if you're in this situation it's too late, but how realisic is this (in your case)?