Having worked on the same targeting mechanisms for protein based vaccines meant to be personalized cancer therapies, and having followed the mRNA vaccines with envy, the benefits are absolutely massive. But there's not a single alternative. In comparison to each type:

Short peptides injection are worse because: minimal immune stimulation, less of a mechanism to train the immune system on the peptide targets, have not been effective.

Viral delivery of mRNA, that makes proteins, or more exotic methods like yeast with modified genomes: this is a traditional vaccine with a custom viral genome with the peptides of interest added as part of the viral genome. This is not directly a protein virus, but it does make the cells it infects produce the peptides. This requires cell culture to grow the virus, which requires a unique clean room per vaccine, which can be impractical and expensive for a custom virus. It's also very very slow to produce, QC, and make sure it's safe. mRNA production is faster, cleaner, safer, just all around better in every possible way.

As for your other questions, sure they are interesting, but get ready to gear up and read tooooons of literature. Most people don't have any of these questions unless they have a deep distrust of the technology, and don't trust that others have bothered to investigate.

Skepticism is good, and if you are truly curious I really applaud you and encourage you to pick up an immunology text book so that you can also read and understand the papers. But mRNA vaccine skepticism has to be the stupidest "skepticism" and falsehoods I have ever seen of a new technology. As the competitor to what I was working on, I must concede that it's better on all metrics, and I am kind of saddened for humanity that all these lies about mRNA seem to dominate over the true and huge technological advancement that has occurred.

If the problem of peptide vaccines is weak immune stimulation, then wouldn't the problem of mRNA vaccines be autoimmunity?

To be fair the media and government are more to blame. By attacking and trying to silence the skeptics during COVID only proved to make what you said worse.

You wont make a very attractive product by shaming, deriding, or forcing someone into taking said product that deals with their health.

Either the skeptic needs the same level of education or an explanation from someone they trust with the level of education needed. You can't convince the skeptics with a sound byte. If they truly believe the government has it out for the entire country. I don't know where you would even begin.

Thinking everyone can be brought to your side with reason is not a logical assumption. Some people no matter how strong an argument will not want to do something no matter the level of evidence or reasoning. Be it their faith or stubbornness and we need to be ok with that.

jailing them, excluding them from society, or forcing them from their jobs to provide to their famalies is how you get people to side with skeptics and does the opposite effect

We can try to optimize how much protein cells will make from the mRNA. The goal is "as much as possible, for as long as possible", but mRNA is not meant to be long lived. And foreign mRNA trying to make its way into cells would be destroyed very quickly without trickery (like the nanoparticle and the pseudouridine).

But either way, medicine works just the same (a surprising amount of the time!) in the cases where the precise details and mechanisms haven't been elucidated yet. If it works empirically, the details are just details.

We have also a lot of cells that do not divide such as neurons, or some cardiac cells.

This patently false, and medical disinformation. It is proven with the Covid vaccines that it spreads to the entire body.

As for whether or not viruses are bad for us, I mean I don’t think we have any choice in the matter anyway, they’re even more numerous than bacteria, and absolutely everywhere.

I wonder how many viruses infect our cells every day vs how many “lipid viruses” are in a standard Moderna Covid shot.

There was another study last year on long covid that found some vaccine-specific spike proteins persisting weeks or months after they should have degraded/been removed by the immune system, but IIRC they didn't find a reason why.

For one, mRNA is easier to produce/manufacture than protein.