The dorico file enclosed.
Untitled Project 2.zip (377 KB)
The reason that your dynamics are not aligned is because you have modified the value for the default distance from the staff for immediate dynamics below the staff (in the Vertical Position section of the Dynamics page of Engraving Options) without making the corresponding edit to the distance for gradual dynamics.
You can’t flip those stems, I’m afraid, because the rests aren’t explicit and cannot be made explicit on percussion staves. However, you should find that it works as expected on non-percussion staves, provided you make sure that the rests are explicit (e.g. you can switch on the ‘Force position and duration’ property to do this).
Oh, it’s true! I didn’t remember that I changed vertical distance only for immediate dynamics… Thank you!
The explanation about the explicit rests solves also my post:
I will post a link to your answer there, in case it helps somebody.
Thank you very much for your help!