I've never noticed any performance degradation by having the bullet base seated below the neck. I figure that some of the powder will stick to the exposed lube, but not enough to worry about. The contaminated powder will probably still burn because the unexposed powder will burn hot enough to light it off as well. Once the exposed lube is coated with powder, it is effectively sealed away from the rest of the powder in the case.
Sorta like putting flour over bisquit dough to keep it from sticking to the rolling pin......
I do however seat my bullets out as far as possible in my single shot rifles and pistols, mostly for accuracy, but not for any concern about the exposure to bullet lube.