I think that what happens in this case is that if you manually input the rotation for the bone, you are acting on the bone rotation before the two constraints are applied. If the constraints that influence it are set to 0 in fact, typing 90 in the rotation field sets the bone to 90.
If you would like to set your bone in a certain exact position and later influence it with with a transform constraint, but without having the constraint move the bone in setup, you could try this sequence:
- Create the bones to be constrained
- Set the bones at the right angle
- Constraint the bones
- Press Match
- Set the mix influence
This is very easy to control when only one bone is constrained to another bone, and it's less viable when you have multiple bones.
Transform constraints - Spine User Guide: Match
The order in which constraints are calculated also influences this position, possibly causing unexpected results if you change it, or if you deactivate one constraint leaving the other active: Constraints: Order example
Also the fact that you checked "local" influences each bone position, further complicating matters: "When checked, the local transform of the constrained bones is modified to match the target bone."
Transform constraints - Spine User Guide: Local
I recommend to try the above steps and see if they let you achieve the desired position, taking into account to also check the order and mix value of other interfering constraints.
