Rick, AI aircraft care nothing about whether their weight or fuel capacity is sufficient for the flightplan assigned. They will happily fly it all the way to the detstination. As long as you don't follow it the entire way, it will load 108 NM (or so) from the arrival airport at its predicted time (based on the speed in the aircraft.txt file) and land just fine. Since most jets, turboprops, recips, and GA aircraft have similar speeds (close enough), substituting one similar aircraft for another is usually quite successful. Yes, substituting a C150 for a 747 would probably not be advisable, I agree.
Since AIFP can swap single aircraft already (and could swap a Cessna for a 747), multiple selection does not create the danger, it simply multiplies the danger *already present* in the program.
The one time I see a good use for this feature is when a flight plan file specifies many "special paint schemes" which I do not want on my computer and want all plans to use the same aircraft in the basic livery. Doing this one by one would be somewhat tedious - multiple selection would make this faster. Since they are all the same aircraft no Cessna/747 issue applies.