I'm surprised you are having that problem. I also enjoy my music through a tweeked to taste PLII music decoder. I use it on two different systems...each with a powered sub but each set up differently.
With my living room system, I use the LF out channels on my Outlaw 990 and let the 990 handle the bass management by setting the levels in there. I have not noticed the bass levels being bumped up using PLII- music.
In my main system with an Integra dhc 9.9, Thiel 3.6 mains and a pair of Velodyne subs, I don't use the LF out on the preamp. I run the mains as full frequency into both the thiels and the velodyne subs and use the crossovers and volume settings on the velodynes to set the balance between subs and mains.
Again, once I have that balance set, I notice no big swings when I switch to PLII music
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Main system:
Integra dhc 9.9
Threshold SA/4e pure class A
Emotiva XPA-1 (2), XPA-5
(2) Threshold S200's
Thiel 3.6 main speakers
(2)Velodyne F1500r subs
Polk RTI28 surrounds
B&W HTM center
OPPO BDP-83 universal player
Samsung HLT6187 led DLP