I notice that phenomenon a lot more (unsurprisingly) when I on occasion (e.g., if no bassoon is present or if the arrangement has no 3rd/bass trombone part) attempt to play something like the bassoon part or Bari sax part on the bass trombone. Below the staff, the result can be startlingly wonkers, while an ocatave up it works reasonably. Also, if I use a cup mute (and in tune!) the bass trombone can work well with or in place of the bassoon at times. I believe you've put your finger on one of the fundamental issues in focusing on the overtones in the tuba low register -- which is very rich in them.
Gary Merrill
Wessex EEb Bass tuba (DW 3XL or 2XL)
Mack Brass Compensating Euph (DE N106, Euph J, J9 euph)
Amati Oval Euph (DE 104, Euph J, J6 euph)
1924 Buescher 3-valve Eb tuba (with std US receiver), Kelly 25
Schiller American Heritage 7B clone bass trombone (DE LB K/K10/112/14 Lexan, Brass Ark MV50R)
1947 Olds "Standard" trombone (Olds #3)