You can einther do a silent install from the standard msi like this:
MSIEXEC /Itoolkit.msi SERIALNUMBER="..." LICENSEPIN="..." ACCESSKEY="..." TKROOTDIR="C:\Program Files\MKS Toolkit" ALLUSERS=1 /qb-
Or you can do an admin installation with
MSIEXEC /a toolkit.msi
and feed Serial, PIN and Access Key to the msi and save those three options from future install commands.
Unfortunately the MSI does not seem to support the creation of msts from external tools such as Admin Studio. You are limited to the following MSI parameters:
REGISTER_DOT_MK=1 - Use MKS Make as the default program for .mk files.
REGISTER_DOT_GZ=1 - Use gzip as the default program for .gz files.
REGISTER_DOT_VPAX=1 - Use Visual Pax as the default program for .tar, .cpio, and .pax files.
SHOW_RELNOTES=1 - Display release notes when installation finishes.
DISABLEADVTSHORTCUTS=1 - Disable advertised shortcuts (no "install on demand").
USERNAME=user - Specify user's name.
COMPANYNAME=company - Specify the user's company.