I still don’t understand the Institute

So I already played the game a few times back when it first came out, I started another playthrough and I still don’t get the institute, I think Bethesda has some thematic and plot goals for the institute so they just make things up to fit those goals even though they end up contradicting themselves.

1. Why does the Institute make synths to replace random people who aren’t in any important positions and don’t even know they are synths? How does this benefit the Institute in any way?
2. How is it possible that there are no tests to tell if someone is a synth but you can pull this big vacuums tube component from their brain? Couldn’t you just do an X-ray? Couldn’t you go to the memory den to have your memory scanned? Couldn’t you just walk through a metal detector naked? Instead it just seems like a forced excuse to have more plot points.
3. Why can the Institute keep Kellog alive and well for 60 years but not Father or anybody else? You don’t even find any of the scientists doing this so they can make more scientific progress?
4. The institute has teleportation yet they can’t just teleport a nuke onto the brotherhood blimp, or Arcadia or the railway base.
5. Father has you go deal with this synth who’s become a raider and tells you that they care about the people of the commonwealth. Yet they clearly do not because their synths kill random people all the time and they kidnap people all the time. So does father know that he shouldn’t be killing random people so he has you deal with the raider synth? If so then clearly he knows that your ideals are different from theirs so why does he appoint you to be the director? If he doesn’t think the institute is evil then why does he try to put on a show for you to convince you that the institute isn’t evil? Seems like a forced contradiction to serve the plot so that you will have a hard time choosing a side.
6. The Institute’s supposedly advanced technology is extremely inconsistent. They don’t have better armor even though cybernetics require extremely advanced material science. They don’t have any better weapons even though again, synths require extremely advanced nanotechnology. Just think about 15th century muskets and modern assault rifles. They work on essentially the same principles except modern assault rifles are more intricate and have stronger materials. Why can’t the Institute just make better versions of existing energy weapons?
7. The last one and this are more nerdy than normal, but this one is more philosophical. It just makes no sense for the institute scientists to still believe in this free will bullshit and how people have it and synths don’t. Not even modern day scientists believe this, especially the ones involved in neuroscience or artificial intelligence. The Institute is so advanced they can manufacture humans indistinguishable from the real thing it just makes no sense what so ever they still believe humans have a magical difference that gives them “free will”.

Original Link – Continuation of discussion