But it pre-prends data I don't need to the lines:

There's the :hide-fields command that will replace fields with a vertical ellipsis. Maybe try something like :hide-fields __REALTIME_TIMESTAMP __MONOTONIC_TIMESTAMP.

But, I would also suggest maybe modifying the logback config to not include the timestamp since it's redundant with the journald one.

But sometimes it breaks and I get a yellow log where most lines show " └ Invalid log message: line at offset 123 is not a JSON-line"

What version of lnav is this?