I can explain. At least, I can explain how we got here. The short answer to your question is: in most cases, you need CTRL/CMD when there is an active command preview. It's not 100% accurate, but it does cover most cases.
For the reasoning behind it, take solid Fillet as an example (which, as a point of historical interest, was the command that we implemented first, so is where we first ran into the problem).
By default, Fusion does not choose a default radius for Fillet, so no preview is generated. While you are in this mode, you can add selected edges to fillet without CTRL (of course, you can use CTRL, it is just not needed):

However, once you drag the manipulator or type in a value, Fusion generates a preview. This confuses the selection UI for two reasons: 1) you can no longer de-select edges that are being filleted, and 2) Fusion needs to prevent you from selecting edges that are the result of the preview itself:

So, because in many systems, CTRL/CMD is used as a way to additively select more things, it seemed reasonable to also bind this to the "preview rollback" function in a command. So, what Fusion does is: when you hold down CTRL/CMD, the preview is rolled back, and you see the model in its un-filleted state. In this state, you can de-select edges that are already selected, select new edges, and also are prevented from selection preview edges:

Then, once this convention had been established, we extended it to most other Fusion commands (at least those that generate a "destructive preview").
Now, we are not claiming that this is the only UI that would solve this problem, and we are continually discussing improvements that might make sense, but for now, this is how it works, and hopefully this sheds some light on the rationale.
Thanks for posting,
Jeff Strater (Fusion development)
Jeff Strater
Engineering Director