Hello Matthew
You make some good points here.
I have considered some of the points that you have made, except the last two ones.
In fact, Winnefred's father is John Crowder, so that could possibly explain the "John" in the transcription.
Which brings me to an important point concerning this type of research, namely the lack of images and the "uneven" quality of the transcribers.
An image is essential in order to be able to check the transcription.
One point you haven't mentioned, is the fact that the census record for "my" Stephen B. may have been lost.
I will see if I can work this problem from the other direction, i.e. find all Brenchley families in Kent, and eliminate obvious non-contenders.
Also I will see if there are any surviving allegations
I was hoping that some research had been done already, but I am not able to find anything useful.