I wonder if you are the person my husband's FTDNA Y DNA match notification showed as2 GD different on 37 marker test.He is at kit# 127187 if you have access to FTDNA site.At Y search he is 7PDQP but I have never been quite sure I entered the test results correctly there and haven't been to that search in awhile.
The markers were 447 which seems to be my husband's personal mutation (marker) that sets him apart from his group that he is listed with on the McKee DNA Group on the FTDNA site.
The other is 607 about which I know zero.
On SMGF, my husband's DNA most closely aligns with Thomas McKee descendants that you mentioned in your post.I have checked it out as far as my search ability carried me and I believe the kinship would have been before coming to what became America.I noted there were many Magee and McGee that were also aligned with that SMGF result.I don't know how we would prove any relationship but I certainly agree that the names have been used incorrectly in so many cases that it seems y DNA is the only way to even begin to figure out the true lineage of the similar surnames in this bunch.
The irony is that folks have always called us McGee.Even my own kinfolks on Christmas card lists from year to year. When we lived near Liverpool, England, folks pronounced the name as McI never McE.I have always remembered that but as I was not into genealogy when we were assigned there I never followed up on it.