Here's the reality:
For constant, reliable voltage with a decent sized sub amp, you are going to need a good quality battery(s), a alternator up to the task, AND the big 3. You pretty much need all three working together to prevent voltage drop.
The Big # upgrade makes a more noticable difference with the larger alternators, your little alt isn't big enough to need larger wire, which is why you didn't see a big difference.
The best bang for the buck fix would be to add a second AGM battery in the back next to the amp, but the ultimate solution will be alternator + battery. You have to pay to play, unfortunately.