import mathutils
from math import radians

vec = mathutils.Vector((1.0, 2.0, 3.0))

mat_rot = mathutils.Matrix.Rotation(radians(90.0), 4, 'X')
mat_trans = mathutils.Matrix.Translation(vec)

mat = mat_trans * mat_rot
mat.invert()

mat3 = mat.to_3x3()
quat1 = mat.to_quaternion()
quat2 = mat3.to_quaternion()

quat_diff = quat1.rotation_difference(quat2)

print(quat_diff.angle)