I'd wager almost every ref would round up to to 6 mins injury time if they had seen 5 and a half minutes of delays during a half, it's almost impossible to calculate the exact time anyway so no ref is ever questioned over the amount of time they asked to be displayed as a minimum, the 4th...
Playing until 95:59 is actually playing 1 second short of 6 minutes injury time. If the signal is for a minimum of 5 minutes injury time the full time whistle should come at 95:00 unless there is a significant delay, even allowing for the goal celebrations there was only about 30 seconds of time...
VAR is allowed to review and award the penalty at the end of the match, when this happens and time is up the ref should have blown once to stop play while the review takes place. Once the review has taken place he then either blows for full time or allows the penalty to be taken and then blows...