Ok. I think I found the answer here: https://bugs.winehq.org/show_bug.cgi?id=35351
This is the file: ~/Library/Application Support/Eve Online/p_drive/Local Settings/Application Data/CCP/EVE/SharedCache/wine/settings.reg
The contents looked like this:
I changed it to this:
Now the option/alt keys work as alt and presumably command also works as control. I had to lock the file though because the first time I tried it reverted to the original form. My guess is the launcher generates this file based on your settings but doesn’t know about these options. Locking a file the launcher is trying to write probably isn’t the best thing to do but it seems to work for now. A better solution is for the launcher to be able to select these options and generate the file correctly.