You have a few options:
1.) License FortiClient EMS (I think that's what it's called) which gives you access to central FortiClient management through your Fortigate. I believe this also gives you access to the FortiClient custom configurator to make custom installs.
2.) Use a custom XML and deploy via script.. This is what we do.
First you configure 1 FortiClient machine and then export it's configuration. Take XML file and make any further customizations and then use a GPO or a deployment tool (we use PDQ Deploy) to install this XML file on each machine by running this command:
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C:Program Files (x86) FortinetForticlientfcconfig.exe
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For specifics, see the last post in this thread:
https://forum.fortinet.com/m/tm.aspx?m=96566&p=
For XML configuration options see Fortinet docs..
http://docs.fortinet.com/d/fortclient-5.4.2-xml-reference