Why would you "nest" keys in the first place? Keys aren't Russian Matryoska dolls.
Just do Ctrl + Alt...
I fail to see what the "bug" is about -- there are no "actual keys or other single units of input" that can't be expressed as
<kbd>text here</kbd> + <kbd>text here</kbd>.
The nested keys is a funny concept that serves no practical purpose, but what would you have it do instead? Automatically add a plus sign that you could just type yourself? Remove the feature so it can't be used because it isn't normally used?
Also, just because I can, have a free tower as a token of my gratitude for posting this enlightening question:
<kbd><kbd>A</kbd></kbd>) looks like a nested key to me, just as it should...
<sub>as a substitute for
<small>for years here, because I have to.