I figured something out.
In the "Local State" file (in the profile folder), under the root object, you can (while Opera is closed) add (or edit if it's already there) a "browser" object and then an object under it named "flags". Under "flags" you create integer types with the names of the flags. For example:
browser {
"flags" : {
"autoplay-policy" : 1,
"save-page-as-mhtml" : -1
}
}
It's a lot easier to do with JSONedit. It's even easier if you go to opera://flags first and set a flag so that the browser and flags objects are already there.
Not all flags will be integer types though. Some may be strings. Integers seem to be used for just simple boolean flags too.
It might not work for all command-line settings though. Maybe it only works for ones listed in opera://flags. For example, this one doesn't seem to work as an on/off like it does when you just pass it to launcher.exe. It may work as a string when you specify IDs to extensions though.
If it doesn't work for all commands, then it'd still be nice that it did.
