Any bacteria that will add off flavors in secondary, would certainly be present in primary. Aside from Brett, lactobacillus, and a few other species of yeast most bacteria should be inhibited/killed by the alcohol levels present in secondary.
Proper sanitation practices and not using wire brushes to clean your plastic fermenters will protect your brew. Better bottles advertise as more oxygen getting into the brew through the airlock/stopper assembly than through the walls of the bottle, so I don't think oxygen is a problem in this case. Unless you're bulk aging for multiple years there shouldn't be a difference.