Got it. I found the issue.

Using that CRT/HDMI video mode switcher added a two line statement to my \boot\config.txt that wasn't there before.

framebuffer_height=1920
framebuffer_width=1080

Not sure why it added this, but as soon as I commented and rebooted, my RetroPie core was back to normal size and not shrunken anymore.

I don't have many statements active in my config.txt so I noticed an extra "list" of other video related stuff at the very bottom. It seemed to have duplicated some of the entries that are in sections above and placed them in the last [all] section of the file. I commented it all out so none of it is active.

framebuffer_height=1920
framebuffer_width=1080
disable_overscan=0
hdmi_force_hotplug=1
enable_tvout=0
hdmi_group=2
hdmi_mode=82

@zachariel thanks

@clyde Thank you very much for your kind words. I actually do have a couple of other ideas I'd like to work on. I'll be sure to post them if I do!

It was solved by updating all installed packages from the Retropie setup tool.