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I've taken an editing pass, mostly moving passages around for better grouping. @Florin feel free to modify anything that I've changed, but I think the only actual rule difference I've made is regarding territories with tied contributions from the two players: since they make no difference to the comparative score of the two players, but I think counting them as positive makes the score that's up for grabs easier to understand, I like splitting the value instead of zeroing it out.

In re-reading and -writing, I still don't understand merged territories. Does "if they can control them" actually mean something? (What stops someone from putting two empty squares next to each other?) Is scoring modified in any meaningful way? (I did replace "8 settler", "5 settler" and "3 settler" territories by "center" "side" and "corner" resp. in the bonus section thinking that's what you meant, but I guess if you have joined or even diagonally adjacent territories they mean different things.)

I don't know how to set up a simulation in musketeer board painter.

In the example endgame, in the newest edition of the rules black would get another move after white passes. I haven't stared at it for any significant amount of time, but I think e5 pushes d5-c5 looks interesting, depending on joined territory rules. It would put three black kings on the horizontal boundary of the new territory, and if it qualifies for the bonus that's worth 240 total (original plus bonus)? Perhaps that also suggests there needs to be a rule about repetition: don't want two opposing royals pushing a single piece back and forth.