How bad is it for the total pupillary distance to be off by 5mm? i checked at home with apps and millimeters rulers and my od's prescription has 68mm and the one at home is 63 - 64mm?

Distances determined by an actual trained providers measurement are generally more accurate than anything you try at home. If you don't trust your provider get a 2nd opinion.

You OD does this every day, multiple times a day and s/he were not doing it correctly, it would affect the fitting of eye glasses. If your eye glasses fit you well, do not be concerned about the difference between in-home measurement and OD measurement. Wish you good health!