Hi, I'm bumping this thread and hoping OP can provide details about how he was able to resolve this with Apple. Same thing just happened to me, almost exactly the same thing down to the new security questions. I'm waiting to hear back from Apple but it doesn't sound good, and she made it sound like it could be days. I'm very uncomfortable with the idea of someone having access to my entire email history of almost 15 years now. Fortunately only old CC info was associated with the account, but my gift card balance is probably depleted. I also saw one of the emails before I was locked out that they changed the CC info. I only recently enabled iCloud so there's only a handful of photos backed up as well, fortunately. Still concerned about them syncing all contacts, emails, etc.
I'm not totally locked out from my email or any Apple ID services. The support person made it sound like if I could provide proof of purchase of my iPad Pro, they can then work with me to resolve on that device. I provided her my order number because that's all I could see in my email, which just happened to have history saved locally from a few months ago where I could see the subject header with the order number, which allowed me to look it up online.
What's really confusing to me is how they changed the security questions, because I thought you have to answer them to change them. It freaked me out enough I created a new email and switched over every account I could remember from my work computer on a secure network. Still, I want to recover my Apple ID because of all the purchased apps and music that would be lost, not to mention some important emails I should have done a better job backing up.