MDT does have the ability to check the boxes. You do this through the customsettings.ini file and the Application GUID's that are in the application folder in MDT. Navigate to your MDT Workbench, Select Applications and double click an application
you want to install. In the General tab on the bottom you will see "Application GUID:" followed by its identifier. Use the mouse and highlight the GUID and copy the contents. Now open up your \\DeploymentShare$\Control\customsettings.ini
file and under the [Default] group, on a new line type
Applications001={Paste the GUID here from your selected application}
You can continue to do this for all of the applications by doing an increment of 1 per application like below:
Applications002, Applications003 and so on.

You can also make the application mandatory by specifying
MandatoryApplications001={GUID}
Jason Santoro A+ Network+