For non EU passengers the boarder guard has to find the most recent Schengen tourist entry and exit stamp and check they didn’t overstay. That takes longer than 2.5 seconds! More like 10. And also ask a couple of questions and stamp it. Though I guess that only needs to happen for half the passengers, the EU ones taking more like 2 seconds. And then if a visa national turns up it can easily add a few minutes delay. It will be much faster once the EU entry-exit system and ETIAS have both gone live.
It is interesting - I've been through both sides several times with my EU partner at both Gare Du Nord and St Pancras. Only on one occasion were they notably faster than my time through and that wasn't at St Pancras. The worst one I had was with the ferry at Ouisterham which took ages.
I can't see the queues have been overlong and the 90 minutes is very much to cover their own backs - I've turned up with 60 minutes before and had no issues.