Bugs should be sent to sequential support. https://www.sequential.com/support/contact-support/
That said, these nitpicks aren't really bugs. The MIDI spec doesn't require that switches send 0/64, it suggests that receivers SHOULD accept 0-63 as off and 64-127 as on. In any case, I don't think the Pro 3 was designed as a generic MIDI controller, where generic switches send generic messages. The instrument sends instrument-specific CC (or NRPN) information which is intended to be played back into the instrument to recall settings or reenact a performance.
Likewise for the octave switches. The octave is represented by 5 values 0-4. Sure, you could subdivide 128 values into 5 groups and equally space the send/receive values. OTOH, it's a lot easier to understand what's going on if you just get a 0-4 AND you can extend/adjust the range later (this particular parameter isn't a great example, but imagine FX indices) without breaking backward compatibility.
Given that Dave Smith is one of the original authors of the MIDI spec, I can imagine that he has at least given the MIDI implementation of his synthesizers a passing thought.
If you need to use the Pro 3 as a generic controller for other gear, you might want to look into MIDI transform software (Max, for instance [disclosure: I'm a developer at Cycling '74], or pd, or MIDI translator or Google "midi processor software") or hardware (like this thing:
https://blokas.io/midihub/). That way, you let the Pro 3 be a Pro 3 and massage the data into a form that's useful for your application.