Hi there.

simple question: is it possible to customize the plugin version of flowplayer like it is with the stand-alone?

I'd like to cofigure it like this:

showStopButton: false,
showScrubber: false,
showVolumeSlider: false,
showMuteVolumeButton: false,
showFullScreenButton: false,
showMenu: false,
controlsOverVideo: 'locked',
controlBarBackgroundColor: -1,
controlBarGloss: 'none'

Sure, look at zp-core/plugins/flowplayer.php of your zenphoto installation. We did not include all those to not bloat the options.
Be sure to duplicate the plugin so that you don't loose changes on update.

I have virtually no knowledge about web development, so my question would be how exactly are these supposed to be used?

The options are all documentated on Flowplayer's site: http://flowplayer.org/player/index.html

Yeh, seen it - problem was that I didn't look close enough in flowplayer.php. My bad.