My theory on this was that Ferrari was simply flat-footed - they were not expecting either Ferrari to make 5 seconds on its team-mate in the space of 2 laps. As such, the call to wait for 2 laps was simply to evaluate the situation and figure out what they needed to do. After all, it wasn't 100% obvious then whether Leclerc had just used a stint's worth of speed in 5 laps total, or if he was in total control of the situation and Vettel was being over-cautious... ...or indeed whether Ferrari would be better off permitting the swapover due to Leclerc being plain faster. Also, if the Ferraris were genuinely similar in speed, then Ferrari might have wanted them together in order to help with overtaking tactics, if they became needed later (we all know how good Ferrari are at making bad strategy calls...)
If the plan was to save engines on the basis they have to last 7 races, or to favour Vettel, giving a 2-lap instruction was pointless because that just kicked the inevitable decision down the road. They might as well have said "We're holding position for the race" the first time, and risked Charles' wrath later if there was any.
If it was a suspicion that the electrical fault might be pending, I'd have expected more monitoring and target-setting in advance of the breakage, let alone the overtake. Apparently there was a bunch of radio from Leclerc's car not broadcast, but it didn't support the notion that Ferrari knew the car was unusually vulnerable to anything until that "There is something strange with the engine" message.
As it happened, Charles didn't get much choice about following the team order because Vettel made a minor error at the end of the next straight...