The clear goes on first to create a perfectly smooth top coat on the playfield before paint and decals.
Think of it like this: It's a layer, like in photoshop. Where virtually anything can be done, and UNDONE, without damaging the playfield underneath. Once you're complete with all the touchups, you lock it in with your final thicker layers of clear to protect it for an eternity.
This is precisely why proper playfield repair isn't for everyone, and why there are more shoddy repairs all over the place. If you're going to do it, do it right once. If you can't do it right, don't do it at all...or alternatively, pay someone else to do it.