Look at the floor of all three pics. The Prometheus Juggernaut has a clean floor, the Covenant Juggernaut has a slightly dirty floor and the Covenant corridor has soil completely covering the floor.
We know that the Prometheus and Covenant Juggernauts were different vessels but they were both in the hangars and thus clean, so we can presume that the ship David and Shaw left in was in as pristine condition as the one that crashed.. There's an opening in the side of the Juggernaut in Covenant so we can presume that nature (wind borne leaves, etc.) has invaded the interior spaces.
The 'new' corridor from Covenant is a different matter though, it looks like a covering of fine sand rather than dried leaves, etc.