Post #97890 from Outlaw Ben (March 8, 2018) clarified something that applies here as well: The EQ is applied only to the source channels, then the crossover diverts the low pass to the Sub. For a stereo source the EQ only applies to the L/R channels. Even though the LF will come out of the Sub, the sub channel's EQ only applies to an LFE source channel. I think this sounds like what you observed?

Good news: you get to EQ for each individual source channel and how it's bass management is handled in combination with the sub. Bad news: this eats up bands in the PEQ on each channel instead of just the LFE channel EQ.