I understand that you have modified Minecraft so that it writes onto the USB drive, but not in the same place for each version. All you need is a symlink to make the Mac side do what you want.
First, delete the Mac side's saves, then in a shell, run the following (based on your comment mentioning the path for Mac; adjust the path to the Windows side as needed):
cd '/Volumes/myusb/Library/Application Support/Minecraft'
ln -s '../../../whatever-the-path-is-to-the-windows-side/saves' ./saves
If I haven't got the Mac-side path right, then make sure the count of ..s is adjusted to match. To test your symlink, run ls saves and you should see your list of worlds.
Most applications, including Minecraft, will follow a symlink as if it is not there, so this should do the trick. (Note that when viewed by the Finder, a symlink appears identical to an alias, but an alias will not function as needed here. An alias is more like a Windows shortcut — it is not automatically traversed by file system calls.)
The file won't regenerate unless you update Minecraft, and needs to be removed only once for a given version. (If Minecraft has an update and you pick "yes" when it asks if you want to update, it'll reinstall a fresh, new copy of the game, with a brand-new META-INF file and none of your mods.)
The META-INF file is a code signing file. Removing it is necessary if you mod Minecraft because the game will no longer match the code signature, and therefore won't start. Removing it prevents the game from checking if it matches, so then it runs fine.
Best Answer
I would not recommend storing it on a USB and playing the game from there. I would recommend transferring worlds when you need to switch computers (I'm sure you can write a script to transfer files from the USB onto the computer or the other way around). However, if you must, i would recommend looking in the Minecraft launcher settings. I am fairly certain you can change the source destination folder in there (along with allocated memory to the game and other semi-useful tweaks).
This guide may be helpful: https://www.pcsteps.com/1346-create-portable-minecraft-usb-stick/