×Short answer is "yes".

To unlock these, you need to find three scrolls throughout the game. After completing Ore Refinery, you can ask the Truth Vessels a question, and you can think up a harder question after seeing each of the scrolls. After finding all three, you can ask the hardest question and unlock a new chapter, which makes the green levels available.

So the only things that matter to this are completing the green levels and finding the harder questions, and advancing the plot.

×RCS Passes open up bonus levels. The first four are puzzle levels with custom elements, the fifth is just a small diversion, the last three are postmastery levels with commentary, bloopers, and a little cut content. The only puzzles on those levels are two rooms with special scripting to show off things people came up with during development. They have nothing to do with the endings, other than being required to see the epilogue scenes that aren't part of either main ending.

Arky Rooms are secret rooms (except for one), and you can earn a challenge if you complete them all. They do not matter for endings.

Rooted Hub Keycards open up two bonus levels. One gives an RCS Pass, the other gives a harder question.

The remaining inventory slots consist of two plot items, the count for the hard questions you've found, and the count for how many of the green levels you've beaten.