It's more likely that they're running the Spec 3 very conservatively, especially considering their speed trap numbers on Friday. You want to be able to assess how the Spec 3 is running in a few sessions (after having not run the Spec 3 since Monza) in order to avoid any surprises during FP3, because then it would be a race to swap PUs in time for qualifying.
The engineers have to make sure all of the software and engine mapping checks out for both qualifying and the race.
On a side note, I'm beginning to wonder if Merc's lack of development on the W10 post-Germany is an indicator that Merc are changing up their concept fairly significantly in 2020.
They need a more efficient car, aerodynamically. They need to be able to figure out how to be kind to the tires via suspension kinematics (perhaps that's why we're seeing the new suspension with Belleville washers), as opposed to just piling on downforce. It's much easier to qualify in front and control the pace than it is to have to fight with other cars on track all the time.