The fact that they own the main domain and the main server means they can choose who to federate with cut off large parts of the network at a whim.
The fact they own the software means they can make it easier or harder to surprise or spread certain messages, and do so in very subtle ways.
Do not confuse open source with safe, something can be open source and be abused even if it's able to be self-hosted.
I just can’t imagine how, honestly! It’s not exactly trivial to programmatically hinder certain messages in a way that others won’t notice and complain about — as they did when Lemmy had hard-coded blacklists for slurs.
If anything, they'd abuse their control of the Lemmy.ml server, like you said.
There are near infinite opportunities for a bad actor to sneak bad code in, so when you're dealing with a bad actor you just don't trust anything they do.
Running code from people who are tied to an authoritarian government is not something you should be doing ever.