I want my road bike to have rim brakes. I want my road bike to have a threaded bottom bracket. I ride mainly in the complete flat land and no mountains anywhere near here but if I live in the mountains I would still have rim brakes. I still happen to run 23mm tires but I am no retro as such. I don't want downtube shifters and probably would go DI2 shifters but my 6800 shifts flawless and not worth it yet.

Sounds like you went to a shop and they told you want you needed. That reminds me when I go to the local shop all the mechanics still would rather have threaded bottom brakes and that is the kind of bikes they ride .I am my own mechanic and wheel builder. Find another shop you need a road bike and I don't think you need that stuff. It is not bad stuff I just don't think you need it.