Not sure if you have done this alignment check or not, but I was involved with laser alignment at GE for years and have some experience in the area. The question about whether or not to break a coupling on a 7EA had come up many times in the US fleet. I believe that the 9E has the same type of Tube coupling as the 7EA. This design is not truely a Rigid/solid coupling but is more of a "Flexible Tube". How much flex, nobody could really tell me. My recommendation to those aligning this type of coupling is to break the coupling before measuring with a laser. If the coupling is in relatively good alignment, laser measurement taken with the coupling bolted and the coupling unbolted should be relatively close. The further out of alignment the rotors are however, the greater the difference between the two measuring methods.
When the tubular coupling shaft is connecting 2 shafts that have a gross missalignment, the shaft will tend to pull the shafts into a straigher line, than they would be in when unbolted, making the measured rim and face readings appear better than they truely are. This is why I do not recommend leaving the coupling bolted when taking readings. When it is broken, you truely know what you have. If you leave it bolted, you really do not know what your alignment is.
The couplings on frame 5 and 6 are truely a flexible design, and using the laser with the couplings bolted is definitely the way to go.
Hope this helps.