For whatever it's worth, I've always only ever used the native Windows build of Emacs, and I've never had any awful problems sharing my config between Windows, Linux and macOS. I'm sure I had to expend at least a bit of effort to make this work initially, but it wasn't enough for the process to stick in my mind, and the ongoing effort doesn't feel like it's added up to much.

(I admit it's added up to more than zero though! Keeping (require 'cmake-mode) working reliably on Windows and macOS has proven a minor annoyance, and fonts seem to require a degree of system-specific attention.)