Thanks to @dtingley11222 being kind enough to help me in DMs, I figured I should share his explanation here too. Worked for me first try without any headaches on my M1 Pro:
The Cherry On Top
What I chose to do, and what I think others might be interested in too, is an app icon that runs this command for you. Using Apple Shortcuts this can be done very easily, and it will even show in Spotlight search.
1) Grab my PKHeX shortcut that leverages a custom launch command: (https://www.icloud.com/shortcuts/2de8268a0547420c86e2c51ca5bea82b) and add it to your library. Follow the setup instructions to add your file paths.
File paths can be easily grabbed by right clicking the app/exe, holding the Option key, and choosing "Copy ___ as Pathname".
2) Once added to your Shortcuts library, right click and choose "Add to Dock".
Optional, change the icon:
3) Remove it from your dock then locate it in your User > Applications folder.
4) Right click and select "Get Info". You can now drag any image onto the icon at the top left of the window to replace it.
5) Done! You can now run PKHeX on your M-Series Mac by running this "app". The icon can be moved anywhere, or even put back into your dock.
Hope someone finds this useful!