A rather difficult installer. For this guide I used as-installer-7.0.2542-full.exe, which is the offline installer available from the company here.

The silent install switch for this software is /passive ( /? works to show the switch options), however the installer has two parts which will not silent install even with the switch:

The xc8 complier

The drivers.

Thus, your install process is as follows:

1. Install the xc8 compiler.

      a.  Start the as-installer and get to the point where the dialog box for the  "MPLAB XC8 C Compiler" pops up.

      b. Navigate to C:\ProgramData\Package Cache and find the compiler installer. For me it was labeled "xc8-installer-2.31"

      c. Copy this into the same folder that you are keeping the Atmel Studio installer.

2. Finish the install of Atmel Studio on a test machine. Be sure to install the complier too. You  should get pop ups for the driver installs. Be sure to hit the check box "Always trust software from this company."

3. Next, we need to export the certs so that the drivers will silently install. 

     a. Run certmgr.msc on your test machine (on later versions of Windows 10, you can just go to "manage computer certificates")

     b. Navigate to "Trusted Publishers" and export anything that says "Microchip Studios" or "SEGGER." Take the default export options. If you have nothing here, you probably didn't hit your check boxes in step 2.

4. Now we make our script. My finished product looked like this:

cd /d "%~dp0"

certutil -addstore TrustedPublisher "microchip1.cer"

certutil -addstore TrustedPublisher "microchip2.cer"

certutil -addstore TrustedPublisher "microchip3.cer"

certutil -addstore TrustedPublisher "microchip4.cer"

certutil -addstore TrustedPublisher "microchip5.cer"

xc8-installer-2.31.exe --installer-language en --LicenseType FreeMode --ModifyAll 1 --unattendedmodeui minimal --mode unattended --netservername ""

as-installer-7.0.2542-full.exe /passive

I hope this helps someone.