It's good you have the red dot to still use. Seems like that's a clue confirming the front sight misalignment whether that's the aftermarket sight manufacturing problem or something on the barrel that got damaged.I don't think there's any barrel damage because the red dot never had to be readjusted.
I'm pretty sure something must be misaligned with the new front sight.
The barrel has a groove on the top that accepts a roll pin which passes through the new front sight post, so, there's no way to adjust/ twist the front sight left or right- the roll pin locks it in.
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You still have 2 methods of zeroed aiming. I'd leave it alone and chalk it up to a learning experience. Otherwise, it's either more experimentation on your part or a gunsmith visit. Or bite the bullet and take off all your mods and throw yourself at the mercy of Ruger who would fix the problem. Ruger might do it for free, though if they don't and they find that you messed up the barrel's sight mount you should not be upset if they charge you something.