If someone gets control of your domain, then yes, there really isn't much difference between a system where a public key in your domain's DNS records is used by clients to tell they are talking to your sites and a system where a certificate issued by LE is used for that.
As you note, once they have control of your domain they can get new certificates from LE for it.
But attacks against the domain owner aren't the only kind of attacks. There are also attacks against the domain's visitors.
Suppose Bob has an old router at home with out of date, buggy firmware that I know a remote exploit for that allows me to change his DNS settings. I change it so that instead of using the DNS servers it get from Bob's ISP via DHCP to resolve DNS requests from the LAN, it uses my DNS server.
My DNS server points your domain to one of my sites instead of yours, where I run my nefarious fake version of your site.
Under the public key on DNS server approach, it's my DNS server, so I can put a public key on it that corresponds to my keys on my fake version of your site, and everything will check out from Bob's point of view.
Under the LE approach, this does not work. To get LE to issue to me a certificate for your site, I have to get LE to use a DNS server I control to resolve your domain.
That's the difference. Under the current system to securely hijack your site I need to compromise your system, your DNS provider, your domain registrar, your ISP, or your hosting provider. Under the keys in DNS approach, I just need to compromise end users.
It definitely makes sense, and I completely understand how this sort of workaround can be necessary to get stuff done. But it's also too bad and I hope there can be a push towards securing DNS sooner rather then later, as it really should be the minimal source of trust in most cases. Having DNS be reliable for that with widespread support would open up a ton of additional new possibilities too, and not just for public websites.
So I guess I'm confused how
would be any worse? Is it that while browsers may not be able to consistently get DNSSEC, Let's Encrypt consistently can for those that use it so it provides a weak bit of OOB workaround? I can see how that might be of some value, but not sure it's worth the trade off. I hope there's at least a concerted effort to someday secure DNS in general, thus making CAs (including LE) obsolete unless they do something beyond domain checks.