"Vim's default are indeed dumb, but what you described is not a vim-specific problem. Walk into any room full of coders and try to use their computers; you'll discover tons of weirdness that can't be explained by anything except by a desire to be treated like a princess."
Yes, shame on those evil coders for wanting to use their own computers in a manner which they find most enjoyable and productive! They must be assimilated! Give me a break.
"Things like rebinding basic shortcuts,"
Again, give me a break. Developers should be allowed to configure their individual machines in any way they wish. Different people work differently.
"reversing the scroll direction (Mac users will get this),"
When you've worked on platforms for decades where the scroll direction works one way, then end up on a platform where it is reversed, what is wrong with changing the new system to work the way you are used to? Yeah, I might decide to get used to the differences, or I might change it because I prefer it the old way, but who cares?
"swapping Cmd/Ctrl,"
again, who cares -- it's their machine.
"using some obscure shell"
I also see no problem with this -- if they prefer it, just let them.
"or even infecting other people's machines with some haphazardly scp'd dotfiles."
This is a legitimate complaint, if the person is leaving stuff behind that screws up the other person's computer. But if the person is expected to work on other peoples machines, then I think a reasonable solution could be worked out. You should try to defer as much as reasonably possible to the person who the machine belongs to. On the other hand, if you are asking someone else to do work on your machine, it seems reasonable to let them copy some dotfiles in order to help them do the work -- as long as they don't affect your stuff.
"This kind of overcustomization is fine if you live in a basement and work on a project alone."
I don't buy the "overcustomization" label. Yes, it is possible to spend too much time customizing things (if, for example, it prevents you from getting your actual work done). However, programmers can make themselves much more efficient by many of these customizations. Different people have different ways of working, and they have different jobs. Vanilla configurations of things like editors are fine, but the ability to customize exists for a reason -- you can make your job easier and yourself more efficient by customizing your tools.
"As soon as you become a part of a team, please stop. You're making cooperation unnecessarily hard and spending company time on an optimization that isn't."
I've worked on many different development teams over the years. At all of those jobs, it was an extremely rare thing to even do development on someone elses computer. Everyone uses their own.
"I sometimes joke that coders who refuse to conform to the industry standards should wear a tiara as an indication they are, indeed, unique snowflakes free from the usual social expectations. It seems to work."
What "industry standards" are you referring to? Is there an ISO standard for vim keybindings? Please. Also, I don't think the whole "Princess" analogy is fair. Just because someone has their own way of working doesn't make them self-absorbed and shallow.
(edited for better formatting)