Is going into HS2PE and rotating the bones the only way to fix the upper spine and shoulders when going from FK to IK?
		
		
	 
Yes. Either from HS2PE or ABMX.
HS2PE retains the data in the scene and can't be animated while ABMX in the chara and can be animated.
You wont have too many things to fix when replacing the chara if using HS2PE.
But in ABMX, the data will reset when replacing the chara, so you need to export the data before replacing then import the data afterwards.
Personally I find using ABMX is better since the number is always round and can be exported. 
I dont like the odd numbers in HS2PE. 346.9373 degree rotation, 1.103 scale, heck no.
Just few things to note :
HS2PE default value based on ABMX current value. While ABMX default value based on number you put in the chara maker e.g. breast size, length, height etc.
It doesn't include the things you can change below it e.g. breast tip, breast scaling 1, 2, 3. These things reflect directly to ABMX.