I think that the problem is you're not learning in order -- like, if you learn functions before variables or data types, you're gonna be confused.

Those things you mentioned actually make perfect sense when you arrive at them with the following assumptions/understandings:

-Western music is founded (not limited to, but founded) on the concept of a "tonal center."

-Western music is founded (again, not limited to, but certainly founded on) limiting the number of available pitches to those available in the equal temperament system, which is to say that the distance between the smallest internal, a half-step, is equal. This means that no tonal centers, or "keys," are favored by the tuning system. In the past certain keyboards might have been tuned to favor pieces written in G, for example. On a "G keyboard," a 5th from G to D would actually be a different number of cents than a 5th from, say, D to A (more on that in a moment).

-Western music also tends to like returning to said tonal centers. Going away from it -- tension, and returning -- release. It's emotionally satisfying and, while I'm only really barely scratching the surface, this concept can explain a lot.

With all this in mind, the "octave" thing makes sense, because for whatever reason, humans like to resolve to tonal centers in a similar fashion -- the basic culmination of all of this is a major key, which no matter what your tonal center is, can be created by starting at a note (let's say C for simplicity), and then counting up the following interval pattern: WWHWWWH, where W = whole step, and H = half step. Therefore, the key of C is C D E F G A B (and then C to complete the final half-step at the top, but we already said that tone so it doesn't need to be included -- but, C to C is 8 notes!).

If the tonal center (or "tonic") is C#, then your major scale is spelled C# D# E# F# G# A# B#. This can answer your B/B#/C question: yes, from the "perspective" of a major scale in the key of C, which unfortunately is what most "layman" musicians tend to think of when they think of a scale due to where music education usually starts, then yes, no B# exists, and the "gap" seems in-congruent, inconsistent, a flaw in the system, like something was bolted on to make it work. But from the "perspective" of C#, then not only does a B# exist, but so does an E#! It's actually a very elegant and, I guess you could say, "self-correcting" system. The lack of a B# from the "C major perspective" is actually a fault of our tendency to start there, but is also an inevitable outcome of a system that is designed to treat all keys equally.

If anything, Western music terminology has a "tonality" bias, which is true, and might be what you're running into and what is confusing you. Once you start really stretching the limits (but this stuff really isn't at all pertinent to this discussion, or really what most people would generally like to listen to...it tends to mostly exist in academic circles), the limitations of the terminology become obvious. But mostly, it perfectly reflects what the vast majority of our music is.

The only thing I'm not quite getting from your post is bringing up backwards compatibility. I get the sense that you're trying to express a fuzzy concept and are arriving at the nearest programming terminology, but I'm not sure what that concept is. Backwards compatibility doesn't really make any sense in the context of harmony. If anything, it technically breaks backwards compatibility with music written before equal temperament was fully adopted, since music written using other tuning systems now sound slightly different. Can you try explaining what you mean by it more? Maybe I can help out.