UPDATE 3/4/21
Took it to another dealer. Regarding both of the engine noises, they think it is related to the cam phasers. Apparently there is a new PCM update for the F150 to address cam phasers. The Raptor update won't be available until May. Ford engineering told them to do the PCM update in May when it's available. If that doesn't fix the issue they will replace the cam phasers. Apparently cam phaser warranty has been extended to 69,000 miles. I'm not sure which models this applies to. The tech seemed to think that a letter may be sent out.