I don't see a way to do this and all the examples i've come across have 2 routers directly connected
I want to measure the packet throughput rate of routers. So I need to send traffic 'through' them and also have packets bounced back to measure jitter, packet loss etc

If I have RouterA->RouterB
It's easy I just use RouterA as the generator, set the source as B and the destination as A then start it. B will take the packets and send them straight back to me

But if its
RouterA->RouterB->RouterC

I don't see how to make it work? If I set the destination as RouterA, B will just immediately send it back to A, it never gets to C
If I set the destination to C, yes the packets get there but C never sends them back so its useless for round-trip performance testing

Is this possible? and if so, how?

It's a bit of busywork, but you could create a tunnel interface (PPTP, L2TP, EOIP, etc.) between routers A and C and test through it.

That's not suited, I need to test routing performance. If it's in a tunnel its not going to pass traffic in the same fashion