Yeah, they really gloss over the fact they have no idea how the TOTP secret key was compromised, which worries me the most.
When it comes to the security of who's hosting my servers, I want a little more reassurance than they shouldn't have access. I need to know that they don't.
The blog post states they're "working towards" these changes, they're not currently in place. It's fairly unlikely that they're using the same secret key as the one they found on the server, but it's fair to assume that they are still using salted SHA-2 for your passwords and the same 2FA setup right now.
They likely won't roll out the major changes until they roll out the "new and improved" Linode dashboard they're coming up with.