Does anyone else from the user interface team have an opinion on this?

Personally I wouldn't expect viewport navigation shortcuts depending on numlock, so leaving that behavior the same by default seems right to me. A preference helps a little bit, but of course does not solve the confusing default behavior with someone that has a keyboard as in the bug report.

The custom numpad keys preference seems too obscure to me, I wouldn't add it.

If Blender were primarily a text editor or IDE, this would make sense (some users prefer these keys for navigation - arrow keys, page up/down, home/end).

However, it has been this way for many years and I don't think this helps to use num-lock in almost all cases.

Num Lock would essentially allow to switch between viewport and keyframe navigation. Probably more useful on laptop keyboards with squished arrow keys.

The custom numpad keys were initially thought as one way to avoid the focus/delete problem for numpad period. Although this can be done way simpler.

Could the custom numpad keys may be useful for addons? Or is there already a way to do this?

No strong opinion, other than what @Brecht Van Lommel (brecht) says. Since you aren't typing numbers, I'm not sure this makes sense for view manipulation.

I'd be in favor of letting users treat numlock/capslock states as (optional) modifier keys. It'd be more in-line with user expectations and it would produce fewer unexpected behaviors than what's proposed here.