Agreeing with Megas and Sooner here. Right-click I always use as a specific "kill this" order on a target ship, so having it default to Eliminate is perfectly acceptable. In a more tactical engagement where I would more likely use a standard Engage order, I'm probably taking my time and planning carefully, so having to click twice doesn't bother me.
Having said that. I have seen Nemo screwing up a few times due to this configuration, and I can sympathise with him - especially since, as a YouTuber myself, I know how hard it is to focus on commentary and the gameplay at the same time - so I would not be against this on principle. However, I would prefer it be a config option if anything.
"shipOrderRightClickDefaultsTo":ELIMINATE # ENGAGE or ELIMINATE
That wouldn't be too difficult, would it?
As for the Help Popups, I would not mind that being a universal game setting - though if that is done, I strongly recommend it remains in the game creation options defaulted to "Enabled" as it is now, because new players definitely need it and won't know to look for it in the settings.