I think on most newer models that issue is dealt with gracefully in the skate designs.
This is what it looks like on SP-TERI boots:
Some boots have ridges that channel the laces and keep it in check. Others put double padding to alleviate it. The boot manufacturers are solving the issue in different ways.
I don't think skating barefoot would have a huge impact on that. Skaters wear such thin socks already.
Skate fit for the skaters boot type and the design of the tongues on that boot are a bigger issue for that. Soft tones are fine if they're designed properly since they don't tend to deform as hardly during use.
I had lace bite issues in my stiffer Klingbiels because the tongues heavily creased which basically forced me to lace a little tighter over it to get the boot to fit over my instep correctly. Even the softer ones crease, though, but I'm not having those issues with these boots because the tab down the tongue makes it extremely hard for the tongue to deform the way those a Klingbiels tongues did:
The stiffer boot with the memory foam tongue padding was horrible because it is virtually impossible to get rid of the crease unless the tongue is redone. The padding is set, and won't loosen up enough to straighten the tongue back out.
The lighter ones were better since the tongue is thinner leather and backed by foam.
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