Hi Starman.
My son doesn't have SPD but does have extreme sensitivities and OEs. I'm also an SI trained OT, so I've checked him out every which way back when I was sure there was something "wrong" with him.
Sensory processing, IMO and those of some current theorists in the field, should be looked at as a continuum. EVERYONE processes sensory information and EVERYONE has problem areas in terms of sensory processing. It's more a question of degree and whether the level or sensitivities or poor registration, etc are interferring with other stuff.
My son has a very vivid visual imagination. He is easily frightened, often fearful of new stuff or strange images, has anxiety issues and is generally very sensitive. I think it is all tied in to the giftedness. When a psychologist spoke to us about his anxiety and keeping an eye on it I asked "isn't it all just part of being gifted?" She responded that it may be but that wasn't the point. No matter what causes the anxiety it needs to be addressed if it is causing disruptions in development or daily activities.
So, my suggestion is to focus on the phobias or anxiety or sensory experiences that are most disruptive for him and just find an approach that works to help decrease those issues. For our son, it helped to work with the school social worker about some imagery - he liked using the visual imagery of a blackboard and him erasing the pictures that "haunted" him. He also does well with distraction and sort of replacing the "bad thoughts" as he calls them with happy ones. We also have found that lots of advanced preparation help. Although over time we have discovered what is the "just right" amount of advanced preparation - because too much info too far ahead of the situation can actually INCREASE his anxiety as he obsesses over it!
My opinion, it's typical of kids like ours. It's all part of the package and is worse for some kids. My son is now almost 8 years old and seems to be getting better in all these areas. So I do think that there is some maturation that helps - as that asynchrony evens out.
Hopefully that will be true for your guy, too. But in the meantime I wuold try some different approaches to help ease his stress and just deal with the phobias, regardless of the cause of them.