This level of proof of control is standard for DV certs, although other providers haven't automated it to the extent Let's Encrypt has, at least not with as high-quality software. One hole in this verification of course, is that 'control' may not actually be 'ownership', it could be someone who's hacked the host or DNS. But that's not unique to Let's Encrypt, it's a side issue, proof of control is standard and accepted for verification for DV certs.
So anyway, that kind of automated proof of control is a lot harder to apply to all of *.example.com, not just an individual host a.example.com. There are likely ways to do it well, but it's harder to do and harder to get right. Is probably why Let's Encrypt, at least for now, is not doing it.
If you control the domain `example.com`, sure. if you just control the single host that `example.com` points to, that doesn't neccesarily mean you control the domain, and in fact DNS contortions are needed to even have example.com point to a host.
