in PCM mode you are sending the discreet channels...
Your AVR then determines how to process cross over and mix those channels.
The LFE (x.1, low frequency effects) channel, is often mistaken for the bass... as many setups have the Sub output labelled LFE...
The issue then is how does your AVR manage the main channel and LFE bass?
If you have your mains "crossed over" (and not set to full range) - then, in theory, the bass from the mains, below the XO frequency, should be sent to the Sub, along with the LFE channel - so the LFE and the Bass from the Mains would be mixed together on the sub output.
Many setups nowadays are based on mains that have no reall bass output, due to everyone having a sub, and smaller "satellite" speakers are easier to place, live with, and get WAF ...
The trouble is, if you then try to run the in "pure" modes (ie: each channel is sent exclusively to its speaker, and no crossovers or mixing is invoked) - you will find the sound lacking in bass.
Typically when you switch from one mode eg: bitstream to another eg: pcm - the AVR is configured to select a specific processing method for each mode by default (on some this is configurable, on others not so much!) - that default mode may be a "Pure Direct" style mode (no XO's) or it might be a blended/mixed mode (use the sub for bass from all channels) - but without further investigation, forum members like myself out in the virtual space, cannot tell.
This is what I would be investigating, were I in your shoes.... what mode is the AVR in when running bitstream, and what mode when running PCM... there is a very high likelihood that the audible difference is in that mode.