Prior to installing the felt paper and the shingles and the boot flashing, (the rubber topped one), take a 12" X 12" section of Grace Ice and Water shield and leave the release paper on. Center it over the pipe and tap a hammer on the inside diameter of the pipe so that the I & W shield gets penetrated all the way through.
Tap lightly and continue tapping around the entire diameter several times if needed.
Now, pull of the release paper and gently slide the I & W shield down to the decking
Notice, by tapping out the INNER diameter of the pipe, that the I & W shield remains slightly bridged upwards in a cantilevered fashion around the entire circumferance of the pipe?
Also, if you are concerned about the longetivity of the rubber seal and wish to prevent it from cracking, install the boot to decking level and mark with a pencil or marker where the top edge seats on the pipe. Remove the boot and smear a high quality sealant, such as NP-1 or Vulkem at that point. Then when you reinstall the boot, also apply the sealant to the top rim of the rubber boot.
This will prevent the damaging rays from the UV of the sun from cracking the top tight seal and allowing moisture intrusion. The I & W shield is a secondary weather-tight backup plan.
Also, if you have any ACE Hardware stores near you, they carry the Oatey hard plastic 1 1/2" boot flashings in stock at the ones near my location, near Chicago.