Some background culled from the Mod Comments:

11-05-2013: DerEider comments; Have been using the "original" PreH and had noted the lack of Tradition culture bonus but had not figured out when it kicked in yet. Thanks for your elucidation.

Also have noted that the Religion 15% build bonus for Ancient & Classical Wonders was not effective for Ggantija and Wonderwerk. Certainly, these should qualify as "ancient".

12-07-2013: from apshai; I am debating whether some of the bonuses would qaulify for the prehistoric wonders of if there should be a separate bonus for prehistoric wonders. Ideas?

12-08-2013: DerEider comments; When I push Religion, I can qualify during Prehistory era for Pantheon Belief "Monuments to the Gods" that gives 15% production bonus for constructing "Ancient and Classical" wonders. The game does not apply that bonus to the Prehistory wonders. There is another 15% bonus under the Tradition Policy branch. I am not sure whether or not that second bonus is applied to the Prehistory wonders.

I guess Civ5 is classifying Ancient wonders as those that may be built after "Agriculture" tech [& maybe before the Medieval techs] is achieved [which is at game start normally]. "After Agriculture" would disqualify the Prehistory wonders. I do not know how this is set. However, I suspect there is a line somewhere in a wonder's definition file that may be used to position it relative to the Tech Tree eras.

As you suggest, it may make sense to have a separate Prehistory Wonder bonus, but that may be complicated by interactions among your mod, the Religion expansion and the Social Policy table. That is WAY beyond my "pay grade".

It seems to me that ANY wonder that may be started before the Classical Era techs should qualify as "Ancient" for the purpose of applying the various construction/production bonuses WITHOUT requiring any Tech prerequisite. Don't know how to accomplish that.