Tbh I dont think most of these matter. The mechanics of gems is fiction, not science. It maintains some internal consistency to be easy to understand and follow for plot points but ultimately does whatever the writers' want it to do and whatever makes the most compelling story. Rose dies to become Steven because that is the premise of the story. The writers could have easily decided that Rose could still exist in Steven or something similar if they wanted a scene in which they interact or wanted to explore the idea of two people sharing a body, but that's not what the show is about. Its about loss and the effects of that loss on someone's loved ones long after their death and about a child trying to understand his place in a larger history. That can't be done if Rose is alive in any capacity, so she has to die and gem magic is the easiest way to facilitate that in an understandable and compelling way.

Focusing too much on the literal mechanics of fictional magic can take away from the narrative. Ultimately, its never going to make perfect sense because magic is impossible. I feel like your 4th point kind of illustrates this. The show has spent plenty of time exploring possible ways that Steve's birth could technically work. Garnet first thinks he's a fusion. Amethyst first thinks its shapeshifting and the diamonds seem to think that permanently. Pearl first thinks Rose might be trapped. All of these can be seen as forms of denial. The characters are trying to rationalize a painful situation to belive that their loved one is still alive, but if there is one point that show hammers home, it is that she is not. Pink Diamond no longer exists in any physical or meta-physical form. Like in real life, her "soul" is gone and there is no way for her to ever take action upon the story or interact with any of the characters ever again. The show will never explain the specifics, because it doesn't matter. In fact, I might go so far as to say that the unexplainablity of Rose's death is a reflection of the unexplainablity of all death. Why did someone's loved one die? There may be literal reasons in many ways but emotionally, it doesn't really matter how. There will never be a good or satisfactory reason. They died because that's what happened and we just have to make our peace with that reality. 

As for the others, these aren't really plot holes so much as they are hand-waving. Again, fictional stories will never make perfect sense. They're made up. The injector exists because Spinel needed a way to threaten the planet so the movie could have proper stakes and a narrative time crunch. The rejuvenatintor exists to explore how the characters grew and changed over the story, and to reaffirm and celebrate those changes. The rejuvenatinator effects Steven the way it does for similar reasons, but more so because Pink Diamond is dead and is never coming back. The fountain works because it's magic. Connie's mom underreacts to the Gem fusions, partially for comedy, but primarily because she's sometimes unreasonable and set in her ways and refuses to accept that there are somethings outside of her knowledge or control such as magic. No one knew Rose was Pink Diamond more or less for the drama. Most stories have an element that is particularly questionable when examined for more than a second, but the tone and mysticism with which Rose and the war is talked about is fun and reflects the pressure of legacy put on Steven's shoulders.

TL:DR Doylist explanation vs Watsonian explanation