I just re-read NM Annual #5. It's actually REALLY easy to ignore the references it drops -- they're not all that specific.
1) the New Mutants are hovering around trying to find Ship. Since Ship was mobile during this time, it isn't a huge deal that it's not where it usually hangs out. Maybe it was off somewhere else briefly.
2) the New Mutants say that it's "good to be back on Earth", and worry that X-Factor might be "still in space". Obviously we know what these are supposed to reference, but they're really non-specific. The NMs DON'T say "it's great to have just returned to Earth from Asgard" and "maybe X-Factor is still in space after Ship unexpectedly launched recently."
Frankly, they could easily be referring to off-panel adventures. The NMs could have just returned from a very brief off-panel trip outside Earth's orbit -- they're glad to be "back on Earth". X-Factor could have had a brief off-panel off-Earth adventure as well -- maybe Ship IS "still in space" from this off-panel story.
3) the New Mutants want to tell X-Factor about "Dani and Asgard" and about "Rusty and Skids". Dani, Rusty and Skids are notably missing. Again, these references aren't SPECIFIC -- they DON'T say "we need to tell X-Factor about how Dani stayed behind on Asgard, and how Rusty and Skids were arrested by Freedom Force." So maybe they're referencing an off-panel adventure as well?
Maybe Dani, Rusty and Skids had just left to go do something Asgard-related. Maybe the New Mutants are just coming back from dropping them off -- which is why they were off Earth until just then. (I'm going with "Dani, Rusty and Skids are fighting trolls on the moon.")
4) Boom-Boom sees the approaching tidal wave and wonders if "Freedom Force is attacking again". Maybe she's drunk.
That's it. Those are all the references we get in the Annual. Nothing that's 100% specific to a previous storyline, no footnotes, no "this issue occurs between X and Y".
Obviously we know what all of these references are SUPPOSED to be referring to. We know exactly what Louise Simonson meant. But, frankly, they're pretty vague and I think that -- if we NEED to handwave them away -- we can.
Where's X-Factor? They briefly left Earth for some reason; the New Mutants are confused because they should have been back by now. (Wherever they went, I guess it took longer than they thought.)
Where are Dani, Rusty and Skids? Off having an adventure somewhere that relates vaguely to Asgard. One which the NMs want to tell X-Factor about.
Why is Cannonball happy to be back on Earth, and why is Boom-Boom talking about Freedom Force attacking again? Maybe they just dropped Dani, Rusty and Skids off on the moon. Maybe they just fought Freedom Force in Earth orbit. Maybe they're drunk.
Do we know where Louise Simonson INTENDED this story to occur? Yes we do.
Can it actually occur there? No, not easily.
So -- if it can't easily occur where it's meant to -- can we ignore, bend or overlook the references that place it there? Yes. Pretty easily.
So let's do that. It sucks for this Annual, but we've done worse things in the past in the name of the bigger picture.
(See also: Dark X-Men: the Confession.)