So everything has a tolerance, and for hand fitting, Omega spells out the procedures and tolerances in Work Instruction 43.
This work instruction covers a lot of ground, so everything from the equipment used, to procedures for fitting hands on all kinds of different watches, procedures for removing hands from normal and delicate dials, procedures for curving hands and when that is required, etc. These work instructions are constantly being updated, so each time they are I download a new version, and keep the old one to track changes.
If I go back to say the 2010 version, there is a tolerance shown using an image. I can't reproduce that image, but I can recreate it...
So the check is done at mid-day. with the hour hand lined up at 12, and the implication is that the red lines indicate the tolerance, although this is never explicitly stated. However on a previous image, they show the tolerance for the calendar jump the same way, which I know is +/- 10 minutes from other documents, and the red lines are shown at 11:50 and 12:10, so we can safely assume that the hand fitting tolerance is +/- 2 minutes based on that image.
So I went through the many revisions of this work instruction I have on file, and in 2020 the image changes. The red lines are gone. Now it just states to check the alignment at mid-day, and shows the hands lined up perfectly at 12.
So what to make of this? Hard to say, but the work instruction was updated in 2021 again, and the diagram still has no lines. Does this mean that Omega has no tolerance so anything goes? No, I would more likely assume this is some sort of error in the updating of the document, than an abandonment of all tolerances for hand fitting.
So when the OP was told that the hands being 3 minutes out were within tolerances, I'm not sure what tolerances the person he spoke to was referring to. The comment that a watchmaker apparently said, that it was "impossible" to line them up due to time train slack, is nonsense, as I and other watchmakers fit hands every day that line up properly. These are however most likely installed by a machine, so if the slack is not properly taken out of the time train, then the hands might be out even if they were 100% aligned with each other when they were installed.
If one can live with this misalignment or not is a personal thing. It's an easy fix, and if the OP has already the case back opened to remove debris, then having it opened again to reset the hands just isn't a big deal. A boutique watchmaker should be able to do this in literally a few minutes.
If the OP wants to pursue this, he just has to find the right person to talk to about it, who will not just say it's within tolerance and send him on his way. Like any other large corporation sometimes you have to work to get something resolved.
Cheers, Al