The way sdtrunk works is that it will by default play audio from any talkgroup ID that isn't in the alias list. In order for a talkgroup ID to be ignored, it either has to be in the alias list and set to not play, or you can add a Talkgroup Range from 0 - 65535 to the alias list and set it to not play which will set the default behavior for any talkgroup ID that isn't individually in the alias list. This is explained here:
https://github.com/DSheirer/sdrtrunk/discussions/1888#discussioncomment-9126173
To accomplish what you are trying to do, I imported the talkgroups for my system from Radio Reference into multiple different alias lists and then I renamed them and toggled the "Listen" switch on different talkgroups in the different alias lists. Although there is no way to clone an entire alias list from the GUI, if you are familiar with XML you can effectively clone the alias list by manually editing the playlist.xml file at C:\Users\[username]\SDRTrunk\playlists\default.xml (make a backup before editing).
In short, the easiest way to accomplish what you are looking for is just to add a Talkgroup Range from 0 - 65355 and set "Listen" to off for all of your alias lists. Then it should work as you expect and you will still hear any talkgroup IDs that are individually in the alias list with "Listen" enabled.
I do wish there was an easier way to quickly switch between alias lists without having to go into the Playlist Editor, change the alias list under the channel configuration, and restart the channel to get the change to take effect.