I run circadian lighting at home using [RELEASE] Day Lights - an iteration of Circadian Daylight, a hub variable, and Room Lighting along with various sunrise/sunset coloring scenes. It's all automated, so that no one needs to adjust anything, but if someone wanted to adjust the level, it would not affect anything at the next transition (which is every 5 minutes due to the app).
As for your questions, there are a few ways to solve these issues. For level changes, the easiest way to solve this is using a Hub Variable to track the level of the lights. Then have Room Lighting active the level of the lights using the Hub Variable. This way, when your transition changes, the level would not be adjusted. When the light turns off, you could have a rule that sets the Hub Variable back to your desired starting level. This way, the lights will always come on at the level you prefer.
Scenes are definitely trickier; though, it depends on what exactly you mean. Are you asking about things like scenes from the Hue app? It's possible, but you need to have Hubitat activate them rather than the app. If you go this direction, then it is possible to limit the activation in Room Lighting when the scene becomes active. This would prevent transition changes (though it would affect the level Hub Variable from above).
Finally, with the dimmer, it all depends on how you want to set it up. I use [RELEASE] Switch Bindings 2.0 to bind switches with my Hue Bulbs along with putting the On and Off in Room Lighting's Means to Activate/Turn Off. It works really well and might do what you need to.
