On FortiGate NAT-T is a Setting of the IPSec Tunnel. It can be enabled in there.
I am not sure if the wizard provides that upon creating a tunnel. Maybe you have to convert it into a custom tunnel after having created it to get access to the option.
an IPSec always must have defined endings. So on the FGT it has to be tied to an Interface.
NAT for internet access on a FGT is done via policy so it will not affect IPSEC (unless you NAT the policy for the traffic over the IPSEC of course).
So the client will have the external ip of that interface of the FGT as remote gateway. You do not need NAT-T because your FGT Internetconnection has NAT, you need it if the client is behind a NAT.