I've deduced that under combination, the axis pass-through point is switched to the origin. This makes no difference in some specific cases, of course, e.g., all axes defined by vector (0,0,1) and points of the form (0,0,z) are identical. In general, however, the current solution seems to be computing/manually correcting the resulting 3D displacements. This is problematic if there are many objects an/or configurations, as there are in this case: 32 leaves, each with a different rotation about a different horizontal axis, and multiple sets of those rotations to test.
The basic case is linked below. The problem can be duplicated by making a rotated copy of CS2 about the axis defined by vector (0,1,0) and point (0,-0.6069,1.02) -- a point on the top, inner edge of the 'leaf' -- by -pi/2 and then combining as B1-CS1-CS2-CS3. The position of the rotated copy in the combined domain will be as if the rotation was done about the axis defined by vector (0,1,0) about point (0,0,0).
https://drive.google.com/file/d/1pdJXExOb1hXCPfdUmpBu2xcqgNhbkof-/view?usp=drive_linkIncidentally, rotating without copying does not work for me. It appears to do some rotation, but very slight relative to the amount specified. Not a big deal to delete originals before combining, but something to note.