In RMMZ, there is a trait to set the 'attack skill', instead of equipping a different skill as the basic attack, try setting a trait on the class to change the attack skill to the same exact copy of the default attack skill with no action sequence, and see what happens.
After doing so, she does indeed attack twice, but both damage appear to be mainhand damage. I even set off-hand multiplier to 0.1 and she is still doing the same as her mainhand attack. This is a bit of progress though, since she does attack twice with a skill that isn't the basic attack command.
Let's work with this first. With this specific case, set the new skill as <dual wield skill> and see if the damage is correct. This shouldn't be the case here, as the engine should treat it as the normal attack at this point, but perhaps it's not.
It appears that the default action sequence command (ACSET: Target action?) would be duplicated normally, but since your action sequence doesn't have that, and uses a custom bunch of stuff in the middle there instead, it's not being repeated properly, while the MECH: Action Effect is being duplicated correctly.
Since you tested all of the original test cases sequentially without resetting the playtest in between, it is most likely that the swing counter is never being reset, even though that might be difficult to see using that one console command I gave you. You can try putting a script call at the end of your action sequence with the following text in it, and it should reset the swing counter completely after the attack:
delete BattleManager._subject._numAttacks
From this I can see that there is definitely something I need to fix about the custom action sequence, I'll need to try to figure out how the duplication of the target action section works in the VS Battle Engine before I can come up with a real solution. As I said above, the YEP BattleCore plugin that it was based on simply repeated the entire target action section, but it doesn't seem like they have sections anymore, at least, based on your sequence there.