Hello,
One thing is really bothering when working on fusion 360 especially after getting to a complex structure is when you create multiple features, then you join two objects (can be through the regular extrude tool, not necessarily the combine tool), while having a third object, but you will have it set as invisible so it wouldn't be included in the "join" process.
Then you go back in the history timeline, do some changes and re-roll the history to see your results, you will find the three objects joined and multiple actions affected by that afterwards (project, etc..). And you will have to find where that "join" happened and fix it.
Why not make sure that each body has its own "serial number" and it the process use that serial number to do different operations?