Maybe I'm not reading your post correctly, but after V1 is reached there is no decision to be made because you are getting airborne regardless. Prior to V1 you can abort and safely bring the aircraft to a stop, but to say to yourself after V1, "gee it still looks like we have more than enough runway, lets disregard that V1 call and keep the jet on the runway" defeats the whole purpose of assigning a V1 speed to your takeoff/data calculations.
The FMS's that I have used on Citations (Collins 3000 and UNS-1) both calculate V1 and Vr by working out what values give a balanced take off for the aircraft weight, temps and pressures. The TODA is not a parameter that is used in the calculation. If departing from a very long runway, it is thus technically possible to abort after V1 and land back on the runway.