The problem is that the rules have changed (for the better). Depending upon which aircraft you're flying, the associated Recognition and reaction times will vary. There was a very good recently running thread in Tech Log ("Calling V1 Early") where these aspects were discussed at length as the thread developed.
In 'the modern era', the 1 second from Vef to V1 remains, but a very important rider is that the Rejected Takeoff must have been initiated BY V1. If you've heard the "V1" call, stopping is not an option, you GO. This is the background to your (presumably modern) Boeing notes wherein you state "Now in my Boeing Flight crew operating manual it says that the abandoned takeoff must occur at V1 at the very latest". That's true.
There's no real conflict between the performance regulations and the Wind-Shear concern. No conflict because it's not considered for the All-Engines or the One Engine Inoperative case. Wind shear is a curve ball out of left field, and impossible to quantify except from the FDR after the event. It can vary from slight to disastrous.
The increased times in the Recognition / Reaction / Full retardation package IS in fact a less stringent requirement, at least from the pilot's perspective, it adresses typical pilot Recognition / Reaction times more realistically. It's certainly more stringent when it gets down to the load that you can carry from a given runway, a commercial increase in stringency.
Generic answers, it all depends upon which generation of aircraft that you fly (and don't forget 'grandfather' clauses that allow more modern versions of essentially the same aircraft to have to meet the 'old' rules.
Regards,
Old Smokey