There is really nothing magic about 4 sq ft per chicken indoors. Personally I think it is grossly inadequate in terms of allowing chickens to behave reasonably comfortably and naturally, if you are in a climate where they will EVER want to spend much of the day indoors; OTOH you can still most often get away with it in terms of avoiding outright cannibalism.
Conversely if you are in a climate where they will truly spend all day EVERY day outdoors -- such as Hawaii, or parts of the Southern US with ample large areas of shade available to the chickens -- then really all you need is enough linear roost space for them at night and "4 sq ft per" may be overkill.
Personally, where you live, I would not feel good about giving them that little indoor space, although if you are fortunate you will be able to get away with it without too much pecking etc; but if you can have fewer chickens or give them a larger enclosed-in-wintertime space, it'd sure be a good thing.
If the nestboxes are high enough above the floor for chickens to walk under them, then they do not subtract from overall square footage. If they are ON the floor, then yes they do, pretty much.
But you know there is nothing magic about a few sq ft in the grand scheme of things. Do what you can, but chickens do not care much if they have 3.8 sq ft or 4.2 sq ft apiece. What DOES visibly affect their behavior, to a considerable extent, is the difference between (say) 4 sq ft apiece versus 8 sq ft apiece, or 15 sq ft apiece.
If you can roof (in a snow-load-proof way!!!) their run and enclose it on 3 or 3 1/2 sides with clear plastic, for wintertime, that will help somewhat.
Good luck, have fun,
Pat