Yes, it does. According to my lawyer, it should be fine to overstay whilst waiting for the processing of your application with pre-approval. With biometrics, supposedly your data becomes visible to SEF at the border control that you are “approved for residency”.
I will be flying out in late February, directly from Portugal to non-Schengen country (through the U.K. to the U.S.). I will update the forum if there will be any difficulties.
Also, there is a separate agreement dating to July 7th, 1983 between Portugal and U.S. that provides automatic 60-day reciprocal tourist visa. Supposedly, it is still valid, though I have had difficult time obtaining its text from the U.S. State Dept. Records Office. I am planning to use that as a “trump card” if all else fails.
Be ready to bail me out… 