So, the problem is solved now, but I don't know what fixed it…
Maybe a RouterOS update?
Not sure.
I noticed the throughput stopped pegging off at 2.5Gbps and would float a bit higher at around 3.5gbps, and that the CPU usage wasn't quite the same as it used to be…
Before all the cores would sit at 0 except one that would peg off at 99% and stay there. Now, while a core or two will sit at 95%, all the other cores will be bouncing around at 2-20% too. Before you'd never see multiple cores do anything like you do now. So I decided to dig in again…
Turns out, most browsers can't push more than about 3.5gbps, and you have to use other software to do speed tests, like SpeetTest dot net's desktop application that they have for Windows.
So, I guess Mikrotik made PPPoE multi-threaded at some point, but I didn't notice right away, because the browser is also a bottleneck too.
It was only after realizing that I suddenly was getting 1gbps faster than I was before that I decided to dig in again and noticed the CPU usage changes and kept digging till I found the other bottleneck.