First a little observation, passenger side....
Reversing the bolt for the toe rod will give you more clearance...
That's why it looks like one side is sitting different to the other, because you have the bolts opposite ways around.
Next, we've found on low cars with certain alignment/coilover/ride height/etc combos that the bolt to strut clearance becomes an issue, standard strut is TIIINY by comparison.
I'd say you need to try lengthening the traction rod, and also in the past I had this issue on a car (our skyline) with standard hubs and I ended up lengthening the traction rod a bit AND grinding a bit off the head of the bolt. It's got a lip on the head, if I remember I just ground it down to remove the lip which gave a couple of mm more clearance along with the traction rods being a bit longer.
Really on a lowered car with camber and toe corrected the traction rod wants to be lengthened anyway to match, or you get mega toe change under load and the wheel ends up a bit far forward in the arch.
So... try lengthening the traction rod and taking a small amount off the head of the bolt. I don't think the hubs look bent, and I don't think this is a "hub related issue", it's just a low car with XYZ combo of parts and settings that needs a bit of tweaking