Skyquake already has jet parts on his body before he scans a vehicle form.
Starscream finds Megatron by following his groans and then discovers Soundwave's drone after hearing its noise. But sound doesn't travel in space.
Since Agent Fowler's jet uses the same animation model as Skyquake's jet mode, it also has Skyquake's legs on its underside, even though it's a real jet, not a Transformer.
Ratchet's giant volcano model seems far too big to have fit through the door of Raf's classroom.