Well if you are going to be pedantic about it... We go by the 1% as a general term, we know the actual number of people it pertains to can fluctuate depending on amount of people residing within the simulation at any given time. We or I also say 1% because it's quicker and easier for all concerned to say '1%' rather than '1.0000000000001% - 1.49999999999 etc... %' any more than 1.49999 etc... would mean it was closer to 98% and could not be 'nearly' 99%

If we take the wording of the Architect as gospel then 'nearly' could range from 98.5% to 98.999999999 etc... % but like I said it's easier for us Humans to say 1%.

We could go by the words of Popper:
E Pluribus Neo will continue to work for the day that everyone can choose to be free of the pods in which the Machines continue to hold 99 percent of humanity unwilling hostages under the sick guise of a "Truce."

But in an attempt at avoiding any further argument about it I'll amend my original statement.

The Cypherites were formed to prevent Zion from waking more than those who don't accept the simulation, a figure determined by the system and the architect to be a tad past 1%, as agreed to by Zion and the Machines in the treaty.