I think that this is a really good feature. However, in order to maintain some level of normalcy within the plugin, it should be included in 'advanced options'. This way, the UI won't be cluttered unless you turn on 'advanced options'. The custom waveform thing being positioned the right also allows for more stuff to be put in the bottom right corner (which would be empty).

I didn't forget about this and sometimes think what to do.

Recently I wonder what if providing this as a separated app like "Magical Wave Memory Plug"

Hmm, that would be interesting. It does kind of seem like a whole new thing since while the previous system attempted to emulate the feel of NES chiptune, this could reach into the realm of Game Boy chiptune.

However, I think putting this inside of a separate window with maybe an advanced menu checkbox that says "Enable Custom Waveform" would be good. Although, I'm not sure if a plugin with multiple windows is even technically possible, and if it is, it might be clunky.

This is a feature I was looking for, and am excited to see some current progress.
I'll provide some of my opinions if it helps:

Currently the window expands to the right, but I'm not sure if it is a good idea or not.

I don't too much about the window expanding to the right. If Waveform isn't selected, then the window will remain normal, and it would only expand to the right if Waveform was selected.

I'm happy with it there, or alternatively it could be placed at the bottom of the window (and thus expand the window down).

UI implementation(especially window resizing) is not in a manner of other features.

I personally don't think we need window resizing for this feature, in my opinion it's okay to leave as is.

If this feature is necessary or not

I would love it!
I think I'd prefer it to be included in Magical8bitPlug2 rather than a separate app, just to make installation easier, but really I don't mind too much.