Alphabet's X has been around for quite a while, too. I don't know how they let him get away with that, unless "X" is perhaps too generic to trademark.
Because Elon's X.com predates Alphabet's X by 16 years...
The reason is probably more-so that Google's "X" isn't apparently a legal entity; its a division within Google. So, it doesn't have consumer sentiment around it, its not a product name they're selling, its not a registered entity, etc. In other words: "Skunkworks" as a term originated from a division at Lockheed, now its a term many companies use, oftentimes in legal & public ways, but Lockheed really doesn't have grounds to stop them from doing so.
[0] https://www.lockheedmartin.com/en-us/who-we-are/business-are...
At Google, these efforts had unlimited funding without much oversight.
At Alphabet, it's basically like running a VC funded startup.