You think that having Skype launch minimized at start up would be an easy and well known Group Policy ADMX file or such… but no no no.
No easy life for you Mr Sysadmin.

Well for you yes, cause I’m writing how I managed to achieve it so you don’t have to bang your head against the desk too much.

Configures Skype’s Own AutoStart

This might be a bit belt and braces and the order 3 item below starts Skype4B on Windows start up already.

• User Configuration
  • Preferences
    • Windows Settings
      • Registry
        • AutoOpenMainWindowOnStartUp (Order:1)

<td>
  HKEY_CURRENT_USER
</td>

<td>
  Software\Microsoft\Office\16.0\Lync
</td>

<td>
  AutoOpenMainWindowWhenStartup
</td>

<td>
  REG_DWORD
</td>

<td>
  0x0 (0)
</td>

All Common option set to No

Minimize Skype

• User Configuration
  • Preferences
    • Windows Settings
      • Registry
        • MinimizeWindowToNotificationArea (Order: 2)

<td>
  HKEY_CURRENT_USER
</td>

<td>
  Software\Microsoft\Office\16.0\Lync
</td>

<td>
  MinimizeWindowToNotificationArea
</td>

<td>
  REG_DWORD
</td>

<td>
  0x1 (1)
</td>

Start Skype with Windows

Again this is a bit belt and braces, I’d go with this option over the first as the only method of starting Skype.

Also note that lync.exe is in the path, so the value data could just be lync/lync.exe so that the officeXX in the path doesn’t matter, for a bit of future proofing.

• User Configuration
  • Preferences
    • Windows Settings
      • Registry
        • Lync (Order: 3)
        • Action: Replace

<td>
  HKEY_CURRENT_USER
</td>

<td>
  Software\Microsoft\Windows\CurrentVersion\Run
</td>

<td>
  Lync
</td>

<td>
  REG_SZ
</td>

<td>
  %ProgramFiles(x86)%\Microsoft Office\root\Office16\lync.exe
</td>

This should then be applied to the OU that the users exist in and Domain Computers be given read access.