I test this on Yakkety Yak in VirtualBox, works normally.
Maybe it's resolved.

Last version of Ubuntu I used is 14.04.
I remembered vlc works normally, but not the same computer.

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https://bugs.launchpad.net/bugs/1625877

Title:
  VLC screen always on top

Status in xorg package in Ubuntu:
  Incomplete

Bug description:
  After new installed VLC on 16.04
  The video screen always on top only while playing with VLC

  the interface disappeared while minimum VLC (video playing)
  video screen remains only

  but the situation is fixed after canceled the option
  "Accelerated video output(Overlay)"

  in Preference > Video > Display

  Reference:
  
https://bugs.launchpad.net/ubuntu/+source/xserver-xorg-video-intel/+bug/1537053

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: xorg 1:7.7+13ubuntu3
  ProcVersionSignature: Ubuntu 4.4.0-36.55-generic 4.4.16
  Uname: Linux 4.4.0-36-generic x86_64
  .tmp.unity_support_test.0:

  ApportVersion: 2.20.1-0ubuntu2.1
  Architecture: amd64
  CompizPlugins: No value set for 
`/apps/compiz-1/general/screen0/options/active_plugins'
  CompositorRunning: compiz
  CompositorUnredirectDriverBlacklist: '(nouveau|Intel).*Mesa 8.0'
  CompositorUnredirectFSW: true
  CurrentDesktop: Unity
  Date: Wed Sep 21 09:23:57 2016
  DistUpgraded: Fresh install
  DistroCodename: xenial
  DistroVariant: ubuntu
  ExtraDebuggingInterest: Yes
  GraphicsCard:
   Intel Corporation Sky Lake Integrated Graphics [8086:1912] (rev 06) (prog-if 
00 [VGA controller])
     Subsystem: CLEVO/KAPOK Computer Skylake Integrated Graphics [1558:6588]
  InstallationDate: Installed on 2016-09-01 (19 days ago)
  InstallationMedia: Ubuntu 16.04 LTS "Xenial Xerus" - Release amd64 
(20160420.1)
  Lsusb:
   Bus 002 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
   Bus 001 Device 003: ID 04f2:b5b0 Chicony Electronics Co., Ltd
   Bus 001 Device 004: ID 8087:0a2b Intel Corp.
   Bus 001 Device 002: ID 045e:07fd Microsoft Corp. Nano Transceiver 1.1
   Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
  MachineType: COPELION INTERNATIONAL CO., LTD. SY Series
  ProcKernelCmdLine: BOOT_IMAGE=/boot/vmlinuz-4.4.0-36-generic.efi.signed 
root=UUID=5e244808-04fe-428e-993a-b6260daede38 ro quiet splash vt.handoff=7
  SourcePackage: xorg
  UpgradeStatus: No upgrade log present (probably fresh install)
  dmi.bios.date: 07/09/2016
  dmi.bios.vendor: American Megatrends Inc.
  dmi.bios.version: 5.11
  dmi.board.asset.tag: Tag 12345
  dmi.board.name: SY Series
  dmi.board.vendor: COPELION INTERNATIONAL CO., LTD.
  dmi.board.version: Not Applicable
  dmi.chassis.asset.tag: No Asset Tag
  dmi.chassis.type: 10
  dmi.chassis.vendor: No Enclosure
  dmi.chassis.version: N/A
  dmi.modalias: 
dmi:bvnAmericanMegatrendsInc.:bvr5.11:bd07/09/2016:svnCOPELIONINTERNATIONALCO.,LTD.:pnSYSeries:pvrNotApplicable:rvnCOPELIONINTERNATIONALCO.,LTD.:rnSYSeries:rvrNotApplicable:cvnNoEnclosure:ct10:cvrN/A:
  dmi.product.name: SY Series
  dmi.product.version: Not Applicable
  dmi.sys.vendor: COPELION INTERNATIONAL CO., LTD.
  version.compiz: compiz 1:0.9.12.2+16.04.20160823-0ubuntu1
  version.ia32-libs: ia32-libs N/A
  version.libdrm2: libdrm2 2.4.67-1ubuntu0.16.04.2
  version.libgl1-mesa-dri: libgl1-mesa-dri 11.2.0-1ubuntu2.2
  version.libgl1-mesa-dri-experimental: libgl1-mesa-dri-experimental N/A
  version.libgl1-mesa-glx: libgl1-mesa-glx 11.2.0-1ubuntu2.2
  version.xserver-xorg-core: xserver-xorg-core 2:1.18.3-1ubuntu2.3
  version.xserver-xorg-input-evdev: xserver-xorg-input-evdev 1:2.10.1-1ubuntu2
  version.xserver-xorg-video-ati: xserver-xorg-video-ati 1:7.7.0-1
  version.xserver-xorg-video-intel: xserver-xorg-video-intel 
2:2.99.917+git20160325-1ubuntu1.1
  version.xserver-xorg-video-nouveau: xserver-xorg-video-nouveau 
1:1.0.12-1build2
  xserver.bootTime: Tue Sep 20 22:21:24 2016
  xserver.configfile: default
  xserver.errors:

  xserver.logfile: /var/log/Xorg.0.log
  xserver.outputs:
   product id                                1191
   vendor                                     LGD
  xserver.version: 2:1.18.3-1ubuntu2.3

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