Are you talking about the crinkles I have highlighted with my picture?

If so I can't see why these should pose a problem, as long as the rubbers seal properly inside the airbox and seal onto the carbs, that's all they have to do.
Inspect them for any cracking or splits, they need to be airtight really.

That (crinkled) outside lip is just there to create a channel to secure the jubilee clip in if I am not mistaken. It may reshape if you removed the rubber tract from the airbox and plopped it into hot water but then in the process you would break the seal of the rubber tract to the airbox...which would not be good.

I have seen this before and I think it occurs when somebody over tightens the jubilee clips which in turn forces the rubber to slightly twist off the carb bell mouth and disconnect. If left they deform in the way you have seen.

I would have thought that when properly refitted the crinkles would pretty much straighten out, the jubilee clips just need a gentle nip up, no need to hang on the screwdriver, just looking to make it airtight and secure. Try and refit, if good, then leave them as is 👍