First, I do not buy that the majority of the early church fathers accepted it as genuine. Origen is among the first to deal with it and was extremely suspicious of it.
Second, one of the reasons, it is said, that scholars reject the work as a pseudopigraphal book is that the author is apparently unaware of Jewish customs of the day. Seeing that this is so, any custom such as custodial marriage that this particular author deals with should also be looked at with suspicion.
As a Protestant, I'm sure you know, what some of these early "Fathers" believed doesn't hold a lot of water for me. Anything that appears past the first 75 or so years after Christ is to be looked at with a certain kind of skepticism, since the primary players are not alive any more. Doesn't mean for sure that it didn't happen; however, I would be suspicious. Likewise, if it isn't found in Scripture then I will not treat it as truth. God preserved what He intended to in Scripture. The Protoevangelium is a forgery, a fake. To make doctrine based upon its words would be a grave error.
Was just reading through Matthew 1 and found another verse relating to Mary's marriage with Joseph. I believe it was suggested somewhere that they never actually married, but Matthew uses the term in 1:18 "before the came together." Sunerchomai. One of these meanings, and one that totally makes sense concerning this translation is "before they conjugally cohabited." If they were never married but only espoused then they would not have been in conjugal cohabitation.