Hi, here are the new results:
#1 and #2 are fixed
#3 is partly fixed now. The new field appears, and if the prefab instance is not changed, its value is there BUT if the prefab instance has a changed value, the value is missing even after starting the game.
#4 is fixed
#5 is fixed
As you can see we are progressing.

Unfortunately, I found a new one that is serious:
#6 - deleting a value from prefab makes the changed prefab instance's identical type values switched (the ext. tree has two, identical type values under each other).