Great question for the Spine community! Preparing assets well is one of the most important steps before you even open Spine, and both of those pain points are very real.
For anyone who wants to dive deeper into best practices around this topic, there is a helpful blog post on how to cut your assets for animation that covers exactly these kinds of challenges, including the importance of drawing hidden/occluded parts:

To give a bit of context on why both of your options matter so much for Spine workflows:
- Option A (layer separation) directly affects how cleanly bones can be attached to individual parts. Complex hair and clothing with overlapping elements can be particularly tricky to isolate cleanly.
- Option B (filling occluded areas) is critical because when a limb or body part moves, the areas that were previously hidden become visible. If those regions are not painted in, you will see empty or broken edges during animation — which is a very common surprise for newcomers.
Both are genuine friction points, and Option B in particular is something that catches a lot of people off guard because it is easy to forget about it until you actually start moving bones in Spine.
Would love to see what the community says — feel free to drop your A or B!