Yeah, those were all reasons I'd considered. It would be useful to know which was the actual reason, though.
I think #1 is pretty much a given. When push comes to shove, the game clearly does not need the original ships (except the Cruiser...) to release, so obviously the priority will be on those that are needed for the SC:O story. We know that #3 is also a factor, but the impression I had was that this was mostly a case of not doing a Kessari Quadrant and continuing their story without them rather than not being able to throw the ships in purely for Fleet Battles purposes. This impression might be wrong.
For #2, I'm inclined to think that the main selling point for GotP is likely to be the story, and FF and PR3 have shown in the past that they're not overly concerned about the ships being used for non-commercial purposes. (Granted, SC:O would be using them for commercial purposes, but nevertheless, the classic ships will already be competing with UQM, Kessari Quadrant for twelve of them, and potentially any versions of Timewarp that might still be playable on modern machines. Depending on how moddable SC:O turns out to be, too, it might not be long until a SC:O mod with the classic ships shows up, although again, that probably files under "non-commercial" while if Stardock did it it would probably classify as commercial use.)
Regardless, knowing the reasoning might be an indication of what might happen in the future. If reasons 2 and/or 3 are the primary reasoning, then it's probably safe to say that we won't see Stardock doing those ships. If reasons 1 and/or 4 are primary, then we might see them in the future as DLC (resolving the royalties issue, as FF and PR3 can then get a hefty chunk of the royalties of the DLC) or as FLC if FF and PR3 are inclined to regard FLC as non-commercial use.