I may have a solution for you. I tried what you tried and got the same result - the command line was grayed out. But I figured a way around that.
You're going to be manually editing one of Delta's config files, so first kill Delta as it might have the config file locked while it's running.
Open Windows Explorer and go to the directory where Delta is installed, probably C:\Program Files\Delta and then go into Config\PSX Games. Here you will find two files for each Delta config, a .nfo file and a .dt2 file. Open Chrono Cross.dt2 in a text editor such as Notepad. Find the Misc Section and then a line that looks like this:
; commandLine= -nocdinc
Change it to what you need (or insert the line if it's not there, just after bios= ), in this case
; commandLine= -noauto
Save, and exit the editor. Restart Delta. If you go to the Misc Psx tab for the Chrono Cross config, you should see the command line entry still grayed out, but containing -noauto instead of what it had before. You should be able to run Chrono Cross from Delta now.