'Way back in prehistoric Glowforge days there was a discussion on this:

The final consensus was that you couldn’t really engrave / score with the GF and then tool your leather.

Well, fortunately for me I hadn’t read that discussion yet, and had the same thought the other day, so I tried it. I cut a circle of PG thick leather, did a draft score (with masking in place) of a rose outline, and then tooled it. You can see the score lines, but I think that has more to do with my lack of expertise with my swivel knife than any issue with the scoring, and a lighter score might be a lot less obvious…

(Be gentle; this is my first attempt at tooling!)