Even though in Transformers: Beginnings they might appear to be in Entry Mode why on earth would they only scan earth vehicles. They have things to do on Cybertron other than in Robot Mode, so wouldn't they just use Entry Modes temporarily? Isn't there a difference?
Disguise? It's a covert mission, so running around in Cybertronian mode is not a good way to do the job since everyone will be onto you rather quickly. Don't forget nobody knew where the Allspark or Megatron was. They could have needed to be there for a while, lying low until something came up. And that's exactly what most of the Decepticons did.
They adopt the alt mode to disguise themselves, so thats the explanation. Even Trailbreaker said so in the second episode of More than meets the Eye, in G1. Disguise is one of the purposes of transformation. Function transformation is another matter.