I seriously dislike the current reloading method. Would it be possible for me to use a macro that simply moves my pointer like 20pxd downwards so I can press esc, press the macro button, then click the reload button and still have it be a legal run, or do all legal runs require full use of a mouse during the menu screens?

I'm primarily trying to bypass accidentally clicking on "achievements" or "stop game" with this method.

I do not see any problems with it. But you'll only lose a few seconds through the hole run, so it's kinda pointless

Well you will only miss it once ever 2-3 runs and macros are not allowed.