Unity doesn't handle well chrome extension windows

[manfreed]

To reproduce:

Install Google Chrome. Chromium might work.
Install the Google Hangouts extension (not the app) (Other extensions that has their own window might have the same issue)

Start the hangouts extension.

I expect Unity to handle the new window as a separate entity: Different icon, not grouped together with chrome. When I close the last chrome window (but the Hangouts window stays open) clicking on the chrome icon should open a new chrome window.

What happens:
First the hangouts and chrome windows were grouped together. I have no idea why this changed, but now they are not grouped together however both acts and looks like chrome icons.

If I move the icon for Hangouts on my dash (or pin it) a new entry will be created in my user's .local/share/application folder, and that ruins opening url-s from external apps.

ProblemType: Bug
DistroRelease: Ubuntu 16.04
Package: unity 7.4.0+16.04.20160906-0ubuntu1
ProcVersionSignature: Ubuntu 4.4.0-45.66-generic 4.4.21
Uname: Linux 4.4.0-45-generic x86_64
NonfreeKernelModules: nvidia
.proc.driver.nvidia.gpus.0000.04.00.0: Error: [Errno 21] Is a directory: '/proc/driver/nvidia/gpus/0000:04:00.0'
.proc.driver.nvidia.registry: Binary: ""
.proc.driver.nvidia.version:
 NVRM version: NVIDIA UNIX x86_64 Kernel Module 361.42 Tue Mar 22 18:10:58 PDT 2016
 GCC version: gcc version 5.4.0 20160609 (Ubuntu 5.4.0-6ubuntu1~16.04.2)
.tmp.unity_support_test.0:

ApportVersion: 2.20.1-0ubuntu2.1
Architecture: amd64
BootLog:

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: Mon Oct 24 09:23:18 2016
DistUpgraded: Fresh install
DistroCodename: xenial
DistroVariant: ubuntu
GraphicsCard:
 Intel Corporation Broadwell-U Integrated Graphics [8086:1616] (rev 09) (prog-if 00 [VGA controller])
   Subsystem: Dell Broadwell-U Integrated Graphics [1028:0632]
   Subsystem: Dell GM108M [GeForce 830M] [1028:0632]
InstallationDate: Installed on 2016-04-16 (190 days ago)
InstallationMedia: Ubuntu 16.04 LTS "Xenial Xerus" - Beta amd64 (20160416)
MachineType: Dell Inc. Latitude 3550
ProcKernelCmdLine: BOOT_IMAGE=/vmlinuz-4.4.0-45-generic.efi.signed root=/dev/mapper/ubuntu--vg-root ro quiet splash vt.handoff=7
SourcePackage: unity
UpgradeStatus: No upgrade log present (probably fresh install)
dmi.bios.date: 04/15/2015
dmi.bios.vendor: Dell Inc.
dmi.bios.version: A05
dmi.board.name: 016MVM
dmi.board.vendor: Dell Inc.
dmi.board.version: A00
dmi.chassis.type: 9
dmi.chassis.vendor: Dell Inc.
dmi.modalias: dmi:bvnDellInc.:bvrA05:bd04/15/2015:svnDellInc.:pnLatitude3550:pvr01:rvnDellInc.:rn016MVM:rvrA00:cvnDellInc.:ct9:cvr:
dmi.product.name: Latitude 3550
dmi.product.version: 01
dmi.sys.vendor: Dell Inc.
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.nvidia-graphics-drivers: nvidia-graphics-drivers-* N/A
version.xserver-xorg-core: xserver-xorg-core 2:1.18.4-0ubuntu0.1
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: Mon Oct 24 09:17:11 2016
xserver.configfile: default
xserver.errors:
 Failed to load module "nvidia" (module does not exist, 0)
 Failed to load module "nvidia" (module does not exist, 0)
 [drm] Failed to open DRM device for (null): -22
xserver.logfile: /var/log/Xorg.0.log
xserver.outputs:
 product id 19528
 vendor SDC
xserver.version: 2:1.18.4-0ubuntu0.1