I would say that if your scanner is set at a certain resolution, it
will scan the same regardless of the area that is to be scanned. I
would only say that the plastic cover over the photos are going to
reduce the quality of the scan by some measure. Do a test and see if
there is a difference between the two. Keep in mind that if you
increase the resolution too much, that every little bit of dust is
going to show up and you'll have to remove it later.
Also, the more resolution, the bigger files it will produce. Check the
file size of various tests first before doing too many. Remember too,
that you can increase the size of a scanned photo with the scanner's
preference settings.
You can scan a 3.5 x 5 into a 5 x 7 quite easily, but almost doubles
the file size!
Paul