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The big difference between grammar and syntax, on the one hand, and punctuation and spelling, on the other, is that grammar and syntax are part of the essential nature of language in the same way that bone and muscle are part of the human body, but punctuation and spelling are human-made, artificial, and arbitrary.

The spoken language is first, and primary.  The written language is a secondary construct, a device for pinning down and freezing in time the transient and ephemeral spoken word.  Spelling and punctuation are imposed upon the language from the outside, in the interest of reducing confusion and supplying at least a few of the non-verbal language components that are lost during the spoken-to-written changeover.  It’s not surprising, therefore, that some these externally-imposed cues can vary from region to region, or even among native speakers in the same region.

A couple of cases in point:

Grey vs. gray.  According to the dictionaries and the handbooks of usage, gray is the “preferred” American spelling and grey is the British one; but “preferred” is not the same as “required,” and a number of American writers use the grey variant.  (Full disclosure:  I’m one of them.  If I’m making up a style sheet for a copy-editor who’ll be working on one of my books, that’s one of the things I’m going to tell him or her.)

The serial comma.  (Also known as the Oxford comma, or the Harvard comma.)  This is the comma that comes before the “and” in a list of items in a series:  “three cheers for the red, white, and blue”; “send lawyers, guns, and money”; “every Tom, Dick, and Harry.”  Some writers believe in the serial comma with an almost religious fervor; others don’t like it at all and never use it.  This one really is a personal choice; just be consistent, and let your copy-editor know.