Having the same issues. I use a 50" TV as the monitor. If my output is 4K (3840x2160) and I load VLC with a custom Skin the Media Player is like a tiny 3" x 4" rectangle and is so small it is unusable. Right now there is no fix for that if you are using higher resolutions. If you go back to a lower resolution you should be fine. It is a scaling issue.
THE GOOD NEWS -
From what I understand this issue will be fixed in VLC version 4.0
They do have Beta versions of 4.0 but you have no support and the builds may not even work.
If you are interested in that you can find it here :
https://nightlies.videolan.org/
Other than that you have to wait for 4.0 coming sometime this year is the rumor.