Hi PDF27
I would do the same as the others suggest and insulate either side of the pipe and only pass the bare pipe through the silicon boot to avoid possible rainwater leaks.
When I did my installation last year, I used the same silicon boot / tile arrangement as yourself, and for the "inside" of the roof, the Armaflex insulation covered the pipe (In my case 12mm S/S Twinsol) right up to where the pipe entered the boot itself. And for the "outside", the pipe was covered first with Armaflex, but then I surrounded the whole set up with an electrical enclosure sourced from RS which has been stuffed with Rockwool to futher increase the insulation of the outside pipes.
(Idea taken from Antmans install. Thankyou Antman

)
Just ensure you used high temp' silicon seal all to prevent water ingress into the enclosure
This setup makes the install / outside insulation very neat, and more importantly bird proof and UV proof (As UV can degrade certain types of foam insulation if exposed for long periods of time to sunlight) And with this set up the enclosure is large enough to insulated / cover my manual bleed valves.
See photos below
So as per the other replies, the only part where the pipe is uninsulated is just where it passes through the boot itself, so only creating a very small thermal bridge and reducing the posibility of rainwater leaks.
Best and kindest regards Al.