the maximum deviation of 2mins 59 seconds?
There in lies your problem.
It is not 59 seconds that is used its +- 30 seconds.
All clocks in ATC are synchronised to UTC.
One of the items you get on start up is a time check to ensure that you are synchronised too.
Take the following scenario
Your Oceanic Clearance is 1700 with a second aircraft procedurally separated 10 min (T & C's apply) behind.
It is possible for you to cross at 1702:29 with the following aircraft at 1707:30.
Separation is still ensured as this +_2 min is part of the safety buffer.
Using your interpretation you think that you should be allowed out at 1702:59 while the following aircraft crosses at 1707:01?