Some interesting points there:
1. You're right, and when not in theatre view, I agree with you that it's better. That's actually an oversight on my part, as having included a "FullScreenPlayer" image with the skin, I then failed to reference it in the xml, so MC falls back on the SlimPlayer image, and so provides more functionality for Cover View. I won't be 'fixing' this
2. They are there for me, which leads me to wonder why not for you. I'm thinking questions such as:
What is your horizontal screen resolution, and how many tabs do you have open, and are any of those tabs using 'drop panes'?
All of these things can eat into the real estate up there, and the first thing to go is always the links when space gets tight.
Mini skins are something I've never been able to get my head round, as in, a long time ago I looked at how others were made, and immediately thought, waaay out of my league, and never went there again!! Sorry.
Do you use the PlayingNow plugin? It can't do transparency, nor shortcut to dsp, but can do everything else. To knock out a skin for that, I'd just need to know your horizontal resolution.
-marko