I would apply for the permits and find out what the inspector has to say.
And, just because there is a legitimate ceiling height factor doesn't mean you can't use spaces in your home for whatever you like. There are many 1 1/2 story homes that have upper level spaces with rather low ceiling height, but many home owners use the spaces for bedrooms or offices or whatever.
It would come in to play when you go to sell. Make sure you disclose that the those spaces might be considered "non-conforming". That usually spells it out to those who are inquiring!!