My own view of this is that these are examples in music notation where "theory" has been allowed triumph over "practice" (and "usability"). There are, from the point of musical theory, some reasons for making use of the notation that is confusing to anyone attempting to read it who isn't steeped in the theory.
It's a difference between being "formally correct" vs. practical. A Bb doesn't (formally) belong in a scale or chord where an A# is (formally) required. It's like a language mistake. It IS a language mistake. You're using the wrong name for a particular pitch in that particular context.
From another perspective, it's quite similar to a software application created solely through the minds of software developers without any consideration for the people who will use it -- the users and their goals and tasks. What you get without good UI/UX design guiding the development is something that's needlessly difficult to use and which will engender frustration and error. In music, you get what -- to normal minds -- appear to be peculiar designations of notes that make reading the music more cumbersome and error prone.
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)