Appreciate the response from the person who suggested I use filters to remove the flickering on Super Metroid's HUD, but any filters I use actually slow the game down, so that's not an option. I assume this is something that will be worked out in time, though, so I'm not stressing.
However, I noticed a more "pressing" issue (a joke you'll get in a minute) with Tactics Ogre: Let Us Cling Together for SNES, which, after some Googling, I discovered has been a RetroArch issue for years. The game doesn't accept any inputs unless you're currently pressing any other button or activating another input. For instance, to select "new game" from the main menu, I have to hold any button or push a direction on the circle pad before it will accept the "A" button. I really hope there's a fix for this... what a bizarre issue.