I've adapted an AutoHotKey script from here which will do what you ask (on Windows - I don't know if there's an AutoHotKey for Linux).
When the script is run, it finds a window with "VLC media player" in the title and makes it 60% transparent and 'unclickable'. To exit the script and reactivate VLC, right click the green H in the taskbar and choose Exit.
If you trust me, a (decompilable) compiled version of this which sets one running VLC instance to 60% transparency and unclickable is here: https://www.dropbox.com/s/to4wrlmnuym9kjb/TransparentVLC.exe
If you don't trust me, want to adapt it for use with Media Player Classic (it's just better =), or just want to learn, install AutoHotKey and run this script: https://www.dropbox.com/s/exj00fpssx761lc/TransparentVLC.ahk
If my links are broken, the AHK code follows:
/*
WinSet_Click_Through - Makes a window unclickable. Written by Wicked & SKAN.
I - ID of the window to set as unclickable.
T - The transparency to set the window. Leaving it blank will set it to 254. It can also be set On or Off. Any numbers lower then 0 or greater then 254 will simply be changed to 254.
If the window ID doesn't exist, it returns 0.
*/
WinSet_Click_Through(I, T="254") {
IfWinExist, % "ahk_id " I
{
If (T == "Off")
{
WinSet, AlwaysOnTop, Off, % "ahk_id " I
WinSet, Transparent, Off, % "ahk_id " I
WinSet, ExStyle, -0x20, % "ahk_id " I
}
Else
{
WinSet, AlwaysOnTop, On, % "ahk_id " I
If(T < 0 || T > 254 || T == "On")
T := 254
WinSet, Transparent, % T, % "ahk_id " I
WinSet, ExStyle, +0x20, % "ahk_id " I
}
}
Else
Return 0
}
#SingleInstance force
#Persistent
;app code starts here
;get window ID for a VLC instance
ID := WinExist("VLC media player")
;set it to 60% transparent and unclickable
WinSet_Click_Through(ID, 0.6 * 255)
;wait until the user quits, then show window again
OnExit, AppEnd
Return
AppEnd:
;set it back to clickable
WinSet_Click_Through(ID, "Off")
ExitApp