Here's my limited experience: For my first PF redo (Sing Along), I didn't clear before touchups, since it just seemed "wrong", but now I regret it.
I leveled the inserts with pipette & clear, Dolphin glaze for leveling & missing wood, frisket & airbush, then keylines. It was painful to sand & level the dolphin glazed areas and avoid sanding off other paint, same for the inserts. Initial clear would have made the sanding much easier & carefree.
Six months later I'm seeing slight depressions around some inserts (where they meet the PF), even though they were sanded perfectly smooth at the time w/no gaps. It almost as if the clear got liquid again and drained through tiny gaps in the original insert glue. I didn't remove and reglue any inserts, but maybe that's the secret. Vid's guide talks about it, but it seemed like a PITA at the time, and I didn't want to fool with decals on inserts after sanding them flat. Maybe the inserts shrunk some more or something? In any case, it still looks pretty good and plays great. Live & learn.
So I'm going to start restoring my Fast Draw at some point this year (hopefully), and I'm definitely going to clearcoat FIRST (2 thin coats), sand to 400 to give it some tooth for paint, do all the touchups, then 2 more clearcoats. From the reading I've done, initial protective coat is so thin it's invisible later, and it's a great idea to protect the original artwork while you're working on it...like when I spilled a few drops of lacquer thinner on the PF - screwed up the paint bad; I had to to frisket & airbrush a whole area that was fine before - Arrrgh!
-M