If you need to run OmegaT on macOS with a set of custom options, it’s possible to do so by running
java -jar --your_options /Applications/OmegaT.app/Contents/MacOS/Java/OmegaT.jar
in Terminal. This is all great, but if your project is located in a folder that macOS considers restricted and asks you for permissions, such permissions will be granted to Java, not to OmegaT. It means that other Java programs will have those permissions too, even if you didn’t intend it to be so.

You can also add those options by editing the Configuration.properties (OmegaT configuration) as well as the Info.plist (Java configuration) files located inside the OmegaT.app package. But it means that OmegaT will run with them each time you start it, which might not be what you wanted (for instance, if you add a custom config folder or start OmegaT with --no-team option, you probably don’t want it be the new default).

A much better way is to start it using open:
open /Applications/OmegaT.app -n --args --your_options

If you have OmegaT.app located elsewhere, just change the path. -n means that it will start a new instance, so you may have more than one projects open at a time. Anything that comes after --args will be interpreted as arguments (options) passed to OmegaT.