I would recommend adding these anytime you have the intake manifold and TGVs off. I wasn't sure if 3mm would be enough to make a difference, but even after drives lasting an hour or two, I could put my whole hand on the manifold without burning myself. Before the spacers, I could probably cook a meal on the manifold.
I regret not taking some temperature readings of the manifold air temp or surface temp before adding these so I can give you some real data.
As far as clearance goes, I have noticed zero change. Zero hood contact, and the top mount intercooler mounts fine.