Wow! this is a really good topic, and I hope many of our learned colleagues step up here.
This is a good opportunity to share ur experience and knowledge with the next generation. This approach applies to so many things.....
Anyway I will start my response off with the fact that I have never heard of any kind of tolerance or expectation for tail shaft alignment that took into consideration the oil wedge, and in addition to that, I never had the time to rely on a software program or lasers to analyze my alignment problems. I have been around when they were tried, but my experience has been different on accepting this technology and the slow process when it comes to using it for ships propulsion. I am not saying the technology doesn't work, it is just that there was never time for it in my life as we "had to go".
The only time I recall this being considered was with my steam license training with turbines and those ships........anyway..
Dial indicators and making allowances for sag (underneath measurement), Straight edges, and feeler gauges are the weapons of choice for me from any range of zero tolerance to what ever you want to try and get.
Doing your alignment checks in the water after a few days was crucial. Alignment readings in the dry-dock are a complete and utter waste of time.
Sometimes on larger diameter shafts water lubed shafts, or even on oil lubricated shafts you will want to make an allowance for the wear down of the tail shaft bearing as it may be a long time for renewal and also considering the environment that the ship works in.
Also in addition to the above, shaft bearing loads for a long tail shaft run such as an offshore supply vessel can be most helpful to you, because the shaft line is so long and it is important to know this information.
From my experience, and I had to approve or direct the align and/or re-align large and small tail shafts. Some of them were caused by incorrect fitting of SKF hydraulic couplings, improperly fitted bolts, poor expectation of coupling tolerances, incorrect line boring, and in fact I even had to align a shaft that was damaged in a tow where the torque overcame the shaft brake and the heat of the friction and subsequent damage resulted in setting up a .065" wobble in way of the damaged blue tempered shaft area.
Ran the ship for a year while I scratched my head and finally figured out a way to straighten it out in situ.....
Anyway, the best rules of thumb come with experience and remember - "the amount of misalignment is directly related to the life-cycle of the bearings associated".
In other words, if the the clutch coupling on a small installation claims that it will take up to .015" misalignment and that is why the shipyard or, err, owners bought it........ remember that if you start out with .013" misalignment, you will wear that wee coupling out a lot faster than if you started it off with .001" misalignment......
So alignment is a bit of a experience and judgement call of what you can tolerate as experienced Chief Engineer and /or Superintendent as opposed to what things are considered in your alignment specification.
Class or state is also involved but there are primarily concerned with the fact that you are actually performing the inspection as opposed to what is acceptable alignment, but the more experienced surveyors with be able to "suggest" what may be acceptable or a target.
This is a great topic for this forum. Thanks.