I got bit by this bug. I chose a name for the company, registered the business and then got the domain name. Then I applied to Apple for the Developer License.
Then I waited and waited. I checked the net and people had spend lots of time waiting. If you register as an individual then that is pretty quick but as a company/business it can take time. Eventually I got in contact them and they said there was a issue.
To cut a long story short, they had a problem with the name I had chosen. I tried to register under a business name called ClockworkApple. I thought it was a cool name and I hadn't thought about the trademark issues. After I submitted I realised that Apple might have a problem with "Apple" but then I found a number of developers that had companies with "Apple" in their name.
Well Apple refused my application. I registered a new company name and domain and then submitted again. This time they didn't like that I called the company "Clockwork Applications" but applied for Clockworkapps. They needed the names to be the same. This was pretty easy to fix and then I got my registration.
It seems that Apple is getting a little more strict on use of their trademarks. And in the App Store world, their word is law.