The traditional x port flickers a bit, (dan just fixed it via xdbe, great!) but proper Ctrl-x, Command-x and just works as everywhere else. RMS politics are stupid, yes, but overall the official port is still the best.
And by "problematic keybindings" you probably mean how most graphical Emacs packages on OS X use the Command modifier key to set the meta bit.
But Mitsuhara Emacs (or emacs-mac as you refer to it) lets you assign any "Emacs modifier bit" (control, meta, alt, hyper or super) to any of OS X's modifier keys (namely, control, option, command or fn) except for the shift key.
So for example if you're on a Macbook, but you are used to the key on the bottom left's being a control key, you would add (setq mac-function-modifier 'control) to your .emacs.
To use the option key as your meta key, (setq mac-option-modifier 'meta).
>The traditional x port flickers a bit
None of the other ports you mention have ever flickered in my experience. And running Emacs under X has the disadvantage that Emacs ends up looking quite different typographically than native OS X apps do.
With the latest XQuartz and emacs 25 only "Use System Font" looks good, before we had much more good fonts. Wonder what caused this regression.