Thank you for your reply Guilin Sun.

I think my main point may have not come through clear enough – How do I compare the results of simulating two different devices with slightly different geometries, when calculating things such as Pabs, refelction and transmission?

Using auto-mesh on each simulation could cause the vertices of the FDTD mesh grid to be different, which could alter the FDTD calculation and provide slightly different results due to effects from inaccurcy of geometry.