Alright, so if I understand correctly, you have all the mechanics working how you want, you just need to force a selection. You tried adding a new tag group which shared Target's group ID, but that ran into duplication errors. Target is a dynamic tag group though, so you are free to make new ones at will with whatever Tag IDs you want. As long as it is defined on something in a common file, the tag should be usable.
Try this. Create an ability which isn't added anywhere, purely to store the new Target tags you'll define. Then define them on this ability, making sure to set the name attribute when defining.
Code:
<thing id="abTagDf"
name="Tag Definition Helper"
description="Just something to define some tags we want to use elsewhere."
compset="Ability">
<tag group="Target" tag="wGrpFlail" name="Flail Weapon Group" abbrev="Group (Flail)"/>
</thing>
Then when you bootstrap the copy of weapon focus, use these newly defined tag. Because there isn't a matching unique ID for the Target tag, the feat won't do anything itself, but it will look right, and if I understand correctly you've already worked around that somehow.