I have not tried to remove/replace these seals or bushings, so this is just a thought. But consider if the added thickness of the ceramic coating within the bores (where the seals/bushings fit) will change the inner diameter enough to make reinstalling more difficult. It may be another area to mask off? However ceramic is not very thick (like powder coating for example) so this may not be an issue. Hope someone else has direct experience to add.
You asked Geekdaddy: "ceramic coating your plenum and did you do the manifolds as well?" When you say 'manifolds', are you asking if the intake runners from the head to the plenum were coated as well as the plenum? I can't answer for Geekdaddy, but considering reducing heat from the exhaust is your goal, it seems to me coating the runners would be more vital than the plenum...they run directly next to the exhaust where heat transfer would be greatest. Likewise for adding heat shields between the exhaust manifold and the intake manifold (as you already mentioned).
As for potential cracking of the ceramic coating I doubt that should be a concern, it is very strong and the clamping loads are not that high.
Just for thought, on another project vehicle (non-Fiat) I had both the inside and outside of the manifolds ceramic coated. Partially for possible added heat shielding, but also to help keep those inner surfaces clean...preventing build up of any carbon deposits, etc. Honestly I've never had it back apart to look (it was recently done) so I can't testify to the results. And I've read mixed opinions regarding the inner surface texture on intake components; one theory is smooth walls allow for better flow, another theory is a slightly rough finish helps prevent fuel from forming droplets. I won't take sides on that. I really did it because I could (the coating company was using my parts for some testing so it was done for free). We also tested the use of ceramic coating on the inside of fuel tanks to prevent rusting. Which brings up a related comment; there are newer ceramic coat products that do not require the specific heat treating process to cure it, they are "air cured". So these can be done at home yourself. The products are not cheap but should be much less than having the parts done professionally. I have some but haven't tried it yet so can't comment on its worth.