Starting the clock after a penalty Federation

[Jim S]

Originally posted by Forksref
"
My conversation with the QB would something like, "We will start the clock on the snap from now until the end of the half." The choice is theirs.

You might start the clock on the snap for the next play, but unless they again try to do something the uses time illegally, you would have to start or stop the clock by rule for any subsequent plays.
The discretion rule does not allow you to change the timing rules per se. Just for the next play.