The main issue isn't the closeness of the stick and buttons. It's that the current set up means has a huge unused chunk on the right of the left joycon and a huge unused chunk on the left of the right joycon, it's weird and unattractive, and certainly not comfortable, for the base controllers that are meant to be used in that manner in multiplayer settings.
But I see what you're saying. Your issue is that the right joystick, in conjunction with the top right shoulder button, needs to be in comfortable reaching distance. Apparently, from what you're all telling me, that means the right stick needs to be in the center of the controller. (But then shouldn't the left joycon 'dpad' be an issue for you if you're also using the shoulder button?).
That's a shame. If they could settle on making joycons universal in design, they wouldn't need to be left and right, they could be sold individually, and you wouldn't have asymmetry. In any case, there are enough accessories, sold separately junk, that this could have been sorted out more gracefully.