The original developer of Transmission and Handbrake are the same IIRC. I hope this is just a coincidence.

Coincidence seems unlikely, doesn't it? Same compromised admin level password, or same vector/hole in 2 places seems likely to me.

Could be the same hacker just continuing to prod his lazy security practices. Or exploiting existing knowledge of his systems to bypass new layers.

Or he exposed himself on criminal hacking forums as an easy mark. But this is purely baseless conjecture.

Were the posted checksums also replaced?

No, the website was not compromised.