So, I tried on the same computer macOS Sierra 10.12.1 (was too lazy to update because I don't use it) and I don't have the Dock problem, but the textures are messed up, too. Then I tried it on another computer, with a Zotac Mini-ITX board with GeForce 9300 chipset, but with a Sapphire Radeon HD6870. But this one has four monitor outputs, my other one has five. There's also no Dock problem in 10.9.5, but the textures are messed up. It would be useful to have more OSx86 users here...
I found a really weird bug, I presume there are only a few people who will have this. I'm using Exposé to get an overview over my windows, and I can access it by moving the mouse in the lower left or lower right edge. My main monitor has 4:3 format, my secondary 16:9. Now I'm doing this: I'm starting Universe Sandbox 2 in 1600x1200 (4:3), then go with Exposé to the System Preferences and set my main monitor to 1920x1080 (16:9 Full-HD). After switching back, Universe Sandbox looks like this:
http://www.bilder-hochladen.net/files/big/c4q7-nr-3799.jpgThe 120 pixels at the bottom are cut off, and on the right are 320 pixels trash.
Universe Sandbox also has problems with the HiDPI modes. My monitors were configured in the following way: Main Monitor 800x600 HiDPI, right monitor 1920x1080.
The older version I have does work, but the screen is too small.
http://www.bilder-hochladen.net/files/big/c4q7-ns-5c41.jpgAlpha19 is really weird: My main monitor remains grey with Dock, the second monitor has a tiny 800x600 image:
http://www.bilder-hochladen.net/files/big/c4q7-nu-bbde.jpghttp://www.bilder-hochladen.net/files/big/c4q7-nt-c49d.jpgAs you can see, this is really in the video memory, otherwise I wouldn't be able to snapshot it with the inbuilt system function, accesseable with command+shift+3.
Both are good demonstrations why there should be a better dual-monitor support. Universe Sandbox should detect the native resolution of the monitor, not the screenmode selected by the user for the operating system. Setting a screenmode should be made from inside the program.