yes, and no.
The things that wind up in the %APPDATA%/Spark/spark.properties file are things specifically saved to that file via code. This means, in code, Spark has to know what to put there. It's possible to have it do this for whatever you want, but it would require source modifications.
Some things may already be in the src/java/org/jivesoftware/resource/default.properties file that you are interested in. Such as the default Look and Feel. Look for:
DEFAULT_LOOK_AND_FEEL=com.jtattoo.plaf.luna.LunaLookAndFeel
and modify to whatever you want. Just make sure you get the correct package name, otherwise spark may freak out and look weird when you start it up. The correct package names are found at:
lines 131 - 173
This would make it so that on first startup, Spark will use this LaF. When spark closes or saves settings, this LaF will be written to %APPDATA%/Spark/spark.properties.
I removed the popout vcards at my company too. I think (if i'm remembering correctly) I had to do this in the source. I'll check tomorrow when I'm in the office for how I made that change. It should be a minor change in the source.