You can bypass EQMule, the "core" of MQ2 is open source still, and there are ways to work around the closed source bits that contain the stuff EQMule has put in place that make it hard to run it on Phinny/Agnarr. If your copy doesn't periodically say "Your integrity has been preserved", then his special module that he forces you to have isn't running and in theory you're "exposed" openly to Daybreak if you're running it on Agnarr or Phinny.
The reality is like everything in software, you can build good doors and walls but people can usually find ways around them. EQMule has been aggressive in breaking known work arounds but that's basically an arms race. The few dudes out there that have a combination of knowledge/desire/motivation to keep making versions that work on Agnarr/Phinny generally have no incentive to share it with anyone else because that a) alerts EQMule to its existence, b) helps their competition (most of these people are krono farmers), and these two things just make more work for them. Once EQMule is aware of a build that works on Phinny/Agnarr he's historically found a way to get a copy of it and figure out what they've done, then break it. Then that person has to find another bypass again.
So the net effect is MQ2 is actually very uncommon on the true-box servers the basic Vanilla compile that EQMule distributes through Redguides ran unfettered on Lockjaw and Ragefire, and it felt like everyone who knew anything was running it on those servers. At one point I was pretty sure there was no MQ2 at all on Agnarr after EQMule said as much (he busted a version that was running on Phinny), but I've seen enough evidence now to know it exists in very small numbers on Agnarr. It wouldn't shock me if some long term, hardcore krono farmer has actually got his own fully functioning "forked" version of MQ2 with custom plugins for his purposes. That would have meant he basically took the fully open source version (back before closed source modules were bolted on to try and get control of it) and has built out/maintained his own fully alternate MQ2 probably over a few years time. That would mean he'd be almost immune to anything EQMule tried to do, but he'd also not be able to piggyback on anything he does either (so he'd have to do his own patches every patch day and etc), if you just have a way to work around the integrity checks EQMule put in you can piggyback on his maintenance of the core source which is less work but probably less reliable too.