LOG Compact FAILED with error: MANIFEST removes non-existing table 15777621,

Do you have a specific question? If so you will have to share what you have done.

Also a little confused on your above output based on you saying:

but the commands are obviously the v20.11.x flags (and the binary is called dgraphv20113).

Making a lot of assumptions here, I would guess when you removed a peer and ran removeNode/ you may not have removed the p, w directories for that peer before restarting it. The reason I say this is the raft ID is given by the zero servers to new clean alpha servers that do not specify a raft ID of their own on the command line, or have it written down in their p/w directories.