I can explain this a bit. When Fusion features compute, they have a set of affected bodies. At compute time, that set does not change. While it seems like, in this case, this logic is obviously wrong, if you step back a bit, you probably don't want this to change. Imagine that you have a cut Extrude, but you have turned off some components/bodies to avoid cutting them. If Fusion were able to change the affected bodies at compute time, then if you turned on one of those bodies and did Compute All, you might find you were cutting bodies that you did not intend to cut. So, yes, we probably could special-case cases like this where the answer is obvious (you want to join all bodies that exist), but even detecting those cases is harder than it seems.
We decided, instead, that if you want to change the bodies affected, you need to Edit the feature. It creates a manual step, definitely, I agree.
To be honest, I don't think that in 6 years of Fusion, I have seen this issue identified more than twice, so it is a pretty uncommon one, FWIW.
Jeff Strater
Engineering Director