You are touching upon some of the reasons why C# is unproductive for us. Because aside from when its "included batteries" decide to in-fight, there is also the parts where the "magic" breaks. This is more anecdotal, however, since it's going to depend a lot on who you and your team are. The guy I was discussing with made a point about C# being very easy to on-board new developers in, which is probably true for them. It has been the opposite experience for us. But I say this as someone who comes from a team where we have very good results on-boarding new developers into our Typescript environment, and I doubt you'll find many people saying that this is a common feat of the JavaScript language.
I didn't particularly mind the new way project files are made up in .NET. It used to be a lot worse too. But at the same time, it can be cumbersome as you point out here and for whatever reason, it's these small annoyances that so rarely get fixed by Microsoft allowing them to pile up. I mean, I just said it used to be worse, and it really did, but then when they made it better they didn't make it great. Which is something I'll just never understand, especially because they did it recently, so it's not like they couldn't have taken inspiration from other languages and done it right.