!st the fortigate could care less if your FGT is policy or route-based mode.
2nd, if your behind NAT ( assuming that' s what you meant ) , than the linux host needs to be made aware or NAT-T in the ipsec.conf global section
3rd if you ment the local-subnet is to be NAT' s b4 going across the table, than deploy iptables with the approp pre-route rule and whatever you NAT it into would be the network you define on the FGT for the " remote" subnet ( linux )
basically you will looking something like this;
conn %default
keyexchange=ikev2
keyingtries=0
conn mygate001_DigiPort-MIAMI
auto=start
left=%defaultroute
leftsubnet=172.88.98.0/24
right=192.168.111.2
rightsubnet=192.34.18.0/24
pfsgoup=modp1024
A stated b4 linux has no concept of your fgt/juniper being policy/routed based mode vpn-ipsec and could care less.
Just match your FGT to the LINUX host in your proposals and ensure your PSK is match. If your on a cert for authentication, it can be quite challenge on your 1st go away but remember to build your certs on the same sign' ing key and then copy that certs over to the fgt and import it.
One tidbit, anything in the global section is just that global, and if you apply a unique parameter under any connections, that overrides the global for that " session"
btw if you make any attempts at a l2tp/ipsec with strongswan or anything opensource, post the cfg for all to see.
good luck