I would say that if “they” edited it out, then they didn’t approve of it ... :-) ...
And “THEY” is an ad agency anyway, and not Apple. Apple just looks over what an ad agency does and if it looks good, they approve it. If I were to get this to come across my desk (and I actually never did hear about this song before this commercial anyway) ... I would simply say, “it looks good; it sounds good; okay - approved.”
It makes no difference if the ad was produced by Apple or an ad agency under contract to Apple.
Apple stands behind every one of their products regardless of whether they are produced by Apple proper, or any of their contractors.
Once they have the Apple name on them, they are wholly the product of the company, and wholly Apple’s responsibility.
I seriously doubt that any ad would have been released without Apple’s approval. If Apple approved the ad, they approved every part of it. If Apple missed the connections, that’s their fault.
But given their primary target demographic, expressing anti-American, anti-military sentiments, even if done stealthily, probably is a net plus for their bottom line.