CommandAliasWithRoot currently fails as it generates a switch case for which there are no switches generated at that location due to being root.

Thank you, I ran the code and checked it.

The choice to allow setting multiple Commands is OK.
Since I think only some users will use it, it's good that it doesn't change for normal use cases.

Regarding the code:
Having the emit for aliases in EmitRunBody feels a bit off, I feel there might be a more appropriate place for it.
Also, the output code unnecessarily indented the case statements.
string[] Aliases probably won't be Incremental,
so an Incremental test is needed (see IncrementalGeneratorTest).