ICAO Doc 9870 refers to the 90 seconds in Chapter 4 regarding the 'Recommendations for the Prevention of Runway Incursion'.
Under the heading 'Pilots' it states "If lined up on the runway and held more than 90 seconds beyond anticipated departure time, pilots should contact ATC and advise that they are holding on the runway." Under the heading 'ATC' it states "Line-up clearance should not be issued to an aircraft if that aircraft will be required to hold on the runway for more than 90 seconds beyond the time it would normally be expected to depart."
Perhaps this has generated the confusion, and if the basis for this query.