With regard to point 1) above, bodies were often sprayed twice after mistakes were made. Leo was a notorious skinflint and would never have allowed anyone to strip and refinish a body, particularly if it were sunburst. The offending blemish would have been buffed out and the body oversprayed with whatever was in the spray gun at the time.
As to point 2), there is plenty of evidence that the importers had bodies oversprayed with red if they arrived in the 'wrong' colour. They would simply have been passed to a car sprayer with the instruction "an orangey-red, please" and he'd get on with it. Again, he'd more likely than not use whatever was to hand rather than order more paint.
For 'everything you ever wanted to know about Fender colours, but felt such a twit for asking', this is the best place you can go to:
http://www.guitarhq.com/fenderc.html