Congrats CT,the Deluxe Bee does indeed rock hard(or not if you want it to)...the extra brightness you're hearing is because of the buffer in the BPB since that side of the pedal, because of the buffer, is not true bypass
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Understand the pedal board real estate thing, but before you think of modding, play around with it more as you JUST got it, AND, yes, you answered your own question...every Bee is different, so as well, dig it for what it is(and the EGDM stack).
I have TWO Deluxe Bee's because they're that good, and I've had my first one for over a year and 1/2, and still IMO it needs nothing.
If you want it darker, run the Nature closer to the CCW side as you know, and play around with the trim pot and how it affects not only the gain, but the range of the drive knob, and where the compression kicks in at higher settings.
Also, if you want darker, maybe think about getting a SBEQ
And yes, I completely agree, the BPB booster is TREMENDOUS...my favorite booster period because of how well it works as an enhancer, and the higher setting boosting qualities that command what you run it into to give up the goods, with little added noise for what you're getting to boot! The best...I had a Gold Klon Centaur years ago..sold it..cool for what it does, but $600-$1000 aftermarket price?!? Uhhmmmm.......no.