Is it a common airline practice to base T/O speeds on the actual T/O weight when an assumed temp thrust is used? Let's say the current outside air temp is 15 C and you have decided to use 50 C as the today's assumed temperature for your takeoff. In this case, use of the T/O weight the assumed temp thrust supports gives you the balanced V1. 

But our company rules are to use the T/O speeds of the "acutual" T/O weight instead of those that the T/O weight the assumed temp thrust applied provides. I assume this rule has been made to give a greater safety margin for a runway overrun in the event of a possible rejected takeoff at the expense of decreased obstacle clearance, since use of the actual takeoff weight invariably brings lower V1, Vr, and V2 speed than when the T/O weight of the assumed temp thrust is used. My question is: is it a common practice among commericial airlines to use the actual T/O weight instead of the assumed temp T/O weight?
You determine the t/o thrust as a function of t/o weight and runway length
Once the t/o thrust is determined you can select the assumed temperature on the thrust limit page on the CDU.

V1 is not the target primary parameter, it is a consequence of the calculation, on modern FMS your calculated value is cross checked with a range calculated by the FMS, that is your calculation could be rejected by the installed FMS unless you may force your value on some models.

A minimum rate of climb is necessary with a speed of V2+10, and at worst V2 with engine failure.

Backward of this Vr is computed.