Though simplest explanation would be the journalist is confused and the sources inside the company aren’t very good.
Plus, Bloomberg journos weren't born yesterday. This story must've been vetted to the highest levels...looks like they've been working for a year or so on it. It's not like they heard it at Starbucks while waiting in line. They are sources and sources.
Now a nation state can provide multiple sources from different alphabet agencies to Bloomberg.
Let's say Bloomberg was correct. Considering the tension between 'the West' and China, and considering how much it's been escalated recently, the consequences of all this are unpredictably catastrophic.
I don't find it difficult to believe that even just to maintain stability for now, various governments would instruct their corporations to lie in a way they haven't done previously.
It's important to keep in mind that for the first time in a while, there's serious tension between China and the West. On top of that, the idea of having China manufacture crucial infrastructure has probably been a concern for quite a while. Making assumptions based on recent history probably doesn't serve us well when predicting our current reality or the future.
So while I'm still inclined to think Bloomberg got things (mostly) wrong, many of my reasons for believing this are based on a 'status quo' that I don't think is the case currently.
I am sure the CEO must know both the hands, if the hands don't know each other. Also that Apple is going to release a strong denial must also have been known to Tim. I don't think that's the case here. Your second possibility looks more plausible.
There are MANY material things that CEOs do not know about TS/SCI information.
Yes, looks like Apple dropped SuperMicro as their supplier in 2017. Why is that $64k question.
Remember also all the denials regarding PRISM.
If this is being correctly handled by the intelligence services (and you can have your doubts on that following these leaks) then nothing further will come out anyway.
For what it's worth, the Register mentions that Apple suddenly dropped Supermicro as a supplier.
The bottom line is that those denials don't really contribute much information.
Two possibilities: Left hand doesn't know (or can't know) what the right hand is doing at Apple. Top secret?
Bloomberg was a victim of a hoax, some nation state (huh huhm!) wants to target China for something so they need a story.
Based on what I've read here these past days, I'm leaning towards the second one. Apple can hire the best or all Infosec companies in the world if security was compromised. In other words, they'd know by now, even if they missed it originally. Cat and mouse and all...