It's not just you , all the OD series are like this. I played a SE+ at the first Chicago land gear fest and the low mids are over powering and extremely fat. I also played a PT 50 at Indoor Storm in North Carolina and had the same issue .I also owned a 3+ SE preamp and had the same issue with that . I actually sold my 3+ preamp for that reason and the horrible pots it came with . I think they were Alpha pots.
There's simply way too much sonic information coming from down below and the more gain you use, the more it gets amplified.I attended the Egnater amp class and one of the things we went over was how to bleed off certain frequencies to ground so that they don't get amplified and tubbed out and this is the kind of mod that . It's exactly the kind of tweak that is done to Rectifiers to tighten up the bass response.
As for what parts to swap, that isn't my expertise . But I am sure that something can be worked out with John to mod the amp.Having played / heard Boneyard's OD prototype tells me that John has the formula already .