So what's the justification for allowing an aircraft to have its wheels on the pavement in the RSA when approaching Vr at the end of its take-off run, but not when slowing to a halt at the end of its accelerate-stop?
I'm not certain that I understand the question, but TORA does not permit that.
Please refer to the cites above.
From the AIM:
(1) Takeoff Run Available (TORA) – The runway length declared available and suitable for the ground run of an airplane taking off.
The TORA is typically the physical length of the runway, but it may be shorter than the runway length if necessary to satisfy runway design standards. For example, the TORA may be shorter than the runway length if a portion of the runway must be used to satisfy runway protection zone requirements.