Understanding the biology behind the way something should theoretically work does not make it more safe. Biology is not like chemistry or physics: results can't always be predicted exactly, even if it's thought that the mechanism of action of a drug/therapy is understood. The human body, as well as the cell, are the results of hundreds of millions of years accumulation of semi-random complexities, and a holistic, complete understanding of the human body to the point where we can accurately predict the results of any experimental or new therapy is not something we are necessarily very close to.
Yes, the vaccine is a great idea and there's really no reason that having a relatively small number of cells express the viral spike protein temporarily to induce immunity should cause problems. As "good" as the idea might be, the fact remains that the vaccine is more complex than that, there are many more components in the vaccine that may be "secrets of the trade," (differences between companies), the mRNA sequences surrounding the spike protein will likely have somewhat significant differences between companies, and, in general, I don't know what the exact long-term effects of all of the components are (since there are many components) and I doubt anyone really does.
Of course, I'm sure extensive testing has been done of mice of the majority of the components of the vaccines and I do believe that they probably are safe, but the truth is that this is the first vaccine of this type being administered on a large scale and we don't know what the long-term effects are. This is an experiment whether you'd like to admit it or not. The only tried and true way to be sure that a drug is safe is through clinical trials, and, yes, clinical trials have show this vaccine to be mostly completely safe so far. I am of the belief that it's probably safe, personally.
But please don't act arrogant and tell me "it's safe if you understand :)))."