how much 3 inch B-vent (double wall) for water heater can be above the roof?
Let me answer my own question as this might help someone else.
After much research and back and forth with Amerivent (thanks Karen O.)tech support I've learned that they feel the SELKIRK guide is the definitive guide on venting  and as per that guide, 5 feet is the minimum vertical (only) height for B-vent with 6 feet recommended and that it doesn't matter if its conditioned or unconditioned space. And of course how high you have to stick up out of the roof penetration is of course dependent on slope and proximity to vertical surfaces and the roof itself, not including other combustion vents.
http://www.selkirkcorp.com/~/media/selkirk/reference-documents/common/file/product-literature/venting/selkirk-rv-type-b-vent/selkirk-sizing-handbook--application-guide.pdf
This gentleman also has some nice pictures and explanations. He doesn't advocate for no-caulk vent flashing boots but according to Oatey they are B-vent rated. (I'm gonna use an Amerivent storm collar with high temp silicone sealant above that Oatey no-caulk vent pipe boot as well) as a precaution.
http://www.summerville-home-inspector.com/comment/reply/129?device=desktop
Also, don't use the generic vent cap Home Depot sells from Amerivent. Use the lock on kind you can get from Amerivent online.
https://www.amazon.com/gp/product/B0...?ie=UTF8&amp;psc=1
Also I've read on Inspectopedia that 16 inches apart for adjacent chimneys is the minimum and obviously you need to leave enough room for the new flashing not to interfere with the adjacent chimney's old flashing.