Game situation: 2:26 left in 4Q, Vikings up 5 and trying to run as much clock as possible. 3rd and 3 at SF 49:

(2:26) (Shotgun) K.Cousins pass short right to J.Addison to SF 36 for 13 yards (T.Hufanga). Penalty on SF-I.Oliver, Defensive Holding, declined.

The Vikings convert and decline the penalty. Without the penalty, the clock would have ran all the way to the 2-minute warning. Instead, the clock was stopped and the Vikings were forced to run another play, thereby giving the 49ers a free timeout:

(2:19) C.Akers left end to SF 4 0 for -4 yards (F.Warner, T.Gipson).

This rule comes from Section 3 article 2 part (e) of the NFL rulebook:

If the game clock is stopped after a down in which there was a foul by either team, following enforcement or declination of a penalty, the game clock will start as if the foul had not occurred, except that the clock will start on the snap if:

the foul occurs after the two-minute warning of the first half;

the foul occurs inside the last five minutes of the second half; or

the offense commits a foul after the ball is made ready for play, and causes the clock to stop before a snap, during the fourth quarter or overtime; or

a specific rule prescribes otherwise.

Since this defensive foul occurred in the last 5 minutes, the clock remains stopped until the next snap. Is this an unfair advantage to give teams to stop the clock? Could a team intentionally commit an offsides penalty to get an extra timeout?