Thank you for the report! And for pasting the variant, I really appreciate it - makes is really easy to give this a quick go on my end.
What I did is go to Edit Variants, 1) click "reckless" button after clicking on the portrait, 2) check "Player max skills" (otherwise it had some trouble facing down two Onslaughts - some changes on my end both to burn drive and to their loadouts etc...), and 3) fight two Onslaughts, assigning an Eliminate on one of them.
I'm not seeing anything related to overloads. I did however notice it being very reluctant to fire its main mixed group at the remaining Onslaught once the first one goes down, regardless of if it's overloaded or not. One of the factors for the Guardian is that the missile hardpoints are so far apart it doesn't think it can land hits with both and so it might think its aim is not good (the AI has no conception of the spread of the Hammer Barrage). Auto-assigning weapon groups eliminates the problem; it'll always fire something and sprinkles in more Hammer shots, too, since they're on alternating and it can fire whichever one it thinks will hit. Or: just removing one of the Hammer Barrages and leaving the group as-is aside from that seems to fix it, too. (I haven't tried it, but I suspect replacing one of them with a Locust - or anything else that doesn't need to aim - might do it, too.)
All in all, this feels like it's an issue with the weapon groupings in this variant. I mean, you're trying to more or less cheese the AI into doing something it doesn't normally do, and if that doesn't work exactly to plan every time - that's kind of a "live by the sword, die by the sword" situation.
Edit: to be clear, I'm not seeing what you're seeing - nothing related to overloads - so what I've said about is regarding the odd behavior that I *did* see. If there is indeed something overload-related, then that does sound like it could be an issue that needs addressing. But, again, didn't see that at all.