That is possibly the most comprehensive explanation of how appearances and materials interact through assemblies I've seen, completely explains why I misunderstood Johnson's solution.
Thank you, this should sort out the issues I have across loads of parts.
I completely agree with your point about the bodies and sub-components affecting the BOM, the reason both appear here is that this whole assembly is a representative model of a part that is purchased from Khrone. (The flanges come pre-attached and as I have a model of them I just dropped it in here rather than modelling one). They didn't have a model available so I quickly sketched this up to check spacings in larger assemblies. The whole assembly has a part-number (linked to an external part index) which is what appears on our BOM's and the body and flanges should never appear.
We currently don't use the BOM that is built into fusion, it was something that I wanted for a long time before it was introduced (am I correct in saying that it is part of the manage extension?) so I wrote some code to manipulate the exported .csv files of parts lists from my drawings into a live BOM system that ties into our part-numbering system and drawing index (all external to autodesk so that anyone in the office can access / print them).
I haven't found any detailed information on how fusion's built in BOM's can be extracted and manipulated (to be transparent, I haven't looked too hard) or organised a meeting with a fusion salesman for a demonstration and, given I expect that it would require me to change my workflow considerably and possibly re-write some code, I'm not sure that I can justify the added expense of the extension.
We build reasonably big renewable energy power plants, so most of my models are one off's for an individual site, or get drawn once and never need updating, which makes most of the iterative production tools that make the manage extension so powerful, inapplicable to us.
Thanks again for taking the time to make that video, it's a massive help, I'll take you advice on the rigid joints.
Is there a quick way to locate the rigid joint between two components? In some of my larger assemblies I have multiple components all aligned to the same point, with an capture position I can just make sure all alignment is contained in one capture position element on the timeline and edit that, but with lots of rigid joints I've often found it difficult to locate the correct joint.