OK, I am happy to figure most of this out so far after sleeping on it.
First: Download your own copy of Boxer and install it.
2nd: Go to resources file as shown in prior post and open it.
3rd: Open Master of Orion 2.boxer

This last step will give you the DOS prompt where you may enter orion2.exe with the switches you want. I found skipintro, goodstart, & hugestart worked;
plants = num (as in planets=5) does not work, perhaps I misspelled or am using it wrong ( Help!).

GOG MOO2 played directly does not allow access to a dos command line and adding a line to the autoexec.bat in GOG's moo configuration files didn't work at least as I tried it.

Playing MOO2 with Boxer downloaded and installed separately from GOG (if you haven't already?) even though you are also using GOG's master of orion 2.boxer file starts MOO2 as if you are a new player so you will have another Hall of Fame other than the one played with GOG only. No big deal in order to get to the DOS command line.

Thanks for asking. I have been wanting to do this for a long time on my Mac. I am new to GOG. GOG with Boxer have made this possible.