As I tested the -SetLimitGroup command both the ways as you mentioned above. It showed the same behavior, the Worker Allow list was empty. It is an expected behavior with the command as we are not specifying any worker in the command.
You would need to specify the worker name in the command to add the worker to the Allow list as:
and your example uses double quotes, C:\>deadlinecommand -SetLimitGroup yeti 12 "" False
But the point I am making is that when you issue that command via a single line on the command line, you don’t get that empty group. But if you use args.txt instead, you do get the empty group.