What is the logic behind having the top Bibles ignore the prioritization rules of canon and advanced priorities?
I'm not sure exactly what you mean.
Very simple - all tools that use "Top Bibles" simply use the first 5 Bible mentioned in the Priority List - ignoring that they don't contain the book in question (e.g. are OT only on a NT passage) or that advanced priority limits them to an inapplicable range or resource. See https://community.logos.com/forums/t/103659.aspx
Edit: Dave says resource specific are ignored ... I'll need to retest.
It seems best if resource-specific rules are ignored, because those rules only get triggered in the event that a hyperlink originates from the specified resource. That's pretty (pardon me) specific, and contrary to the general spirit of "Top" in "Top Bibles."
Otherwise, Top Bibles is pretty dumb straightforward, and probably due for some design attention.
Dave's right.