I’m not running rokbox (that was drokkon’s solution). I did the plugin dance again (disable, re-enable one by one) and actually pinned this problem to Jetpack, strangely enough.
With Jetpack disabled, the plain text embed (a Youtube URL) respects the max width set under Media Settings. With Jetpack enabled, that value is ignored and the video is embedded at full 640px width.
I’ve confirmed this on another site as well.