Azure Fortinet Application And Virtual Machine

Hello,

at the end of the day they are exactly the same product: you will have one (or more) Fortigate VMs, it is not SaaS.
The first use case (that says VM) only covers PAYG model and it creates a single VM that you will need to deploy in your infrastructure and create all the resources needed "around" this VM, like VNET or Subnets.
On the second option (the one that says Azure Application, which may be misguiding) you have the option to deploy once again a single VM in PAYG (and you can see that the hourly cost is exactly the same) or choose among some deployment options where 2 VMs will be deployed along with all the infrastructure and load balancing or HA technics between the VMs. On this second option you can also use a BYOL model.

Again, to be clear: both deploy Virtual Machines, no SaaS in these 2 alternatives.