I have worked with some engineers that like to assign high stiffness modifiers to rafts to get conservative flexural and shear design of foundation. Assigning modifiers would increase amount of rebar in your raft. I personally think that this is good practice as nothing is perfectly rigid and cracking in inevitable, which would result in loss of inertia and high flexural stresses.
The general procedure is to create two models. One with no stiffness modifiers and one with modifiers for foundation/ raft. You should use the first model to calculate piles reactions and the second to do flexural and shear design.
Thanks.