Yeah it's ok I know exactly what you mean, i've experienced the same thing. But I managed to solve it.
My first set of boots (Kaiju) were doing that too - deforming slightly where the thicker part of the buckle was.
I found that adjusting the toecap position side to side and also getting it over the correct part of the toe helped.
But what made it go away completely was getting wearing the strap completely as a top strap not cap. I find that config much more responsive because the pressure is directly over the ball of the foot, sot it really holds the foot in place and you don't need to crank it.
However, I've since go the same boot a half size smaller and it does not deform at all wearing cap. Tried if for a few runs and its was fine. But still prefer the extra response of wearing them top by a mile.
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