I think another difference is the split between Cooper in "real life" and lodge Cooper. Leland wasn't split up in two like that, there was no "good Leland" trapped in the lodge, both good and bad were present in one body.
I believe Bob is something that makes the base, animalistic urges we all have take precedence. Bob is not limited to matter or form, it is a state of mind. So Bob is expressed differently by its different hosts.
It isn't even really "Bob", I believe that is just the name Laura gave it because she knew a Bob and a Mike, and subconsciously assigned those names to those dreams and feelings, the urges she had as well. I think even the Red Room could have been shaped by Laura's dreams, all created by her as an elaborate fantasy world to make sense of the abuse she suffered. There is also the angel in Fir Walk With Me, which was on a painting in Laura's room I think, and which later materialized in the Red Room as Laura died. The (black) lodge is older though, the red room is just the way Laura "painted" it.
Lynch has an interest in Buddhist philosophy and I believe there is a theme of struggle with the urges of greed and desire, running throughout the series. This was shown again in the new series when evil Cooper says "You follow human nature perfectly", namely our lower urges, and when he said he doesn't need, he just wants. Another moment that struck me as confirming this was Sarah Palmer watching the nature documentary with the gruesome footage of lions devouring their prey, which also reminded me of the brutal way the ghost form from the glass box killed its "prey".