Maartenn100,
Let's see this helps any. I think you are Philosophically disturbed that you can't stand in a 2nd separate universe, observe time in this one, and therefore can't relate the passage of time to a standard clock of the 2nd separate universe to say "Ah Ha, now we have an 'Extra-Universal' time measurement that gives a more meaningful conveyance of time for us." Even if you could do this, I don't think expressing the exact same length of time, with an extra-universal clock will have any impact on the calculations.
You're getting wrapped around the axial by what time is to begin with. All you're doing with the use of a time measurement is relating it back to something a Human can understand. We're currently using the time it takes for Earth to circle the Sun one time as a way of conveying lengths of time. Sure, it's extremely arbitrary, and that DOES NOT MATTER. So, if it takes 1,000,000 years to travel to a particular star from Earth (and only from Earth), you can then imagine the time it takes for the Earth to circle the Sun, then imagine 1,000,000 of those time segments stacked one after another.
So, you will next argue that this number might be 1,000,001 years to some observer elsewhere. Ok, no problem. The information necessary for the adjustment did not vanish from our universe. Once you have all the information about the remote observer, you make an adjustment to turn the 1,000,001 year measurement from the Andromeda Galaxy observer and convert it back to what it would mean over here on Earth. You ARE NOT missing A YEAR of time. The time it takes from Earth to this star is the time it takes. That someone else observes something different is irrelevant. It may appear to an Andromeda Galaxy observer that it will take 1 extra year than what the Earthlings are predicting, but this is an illusion that can be backed out of the measurements to get to real time it will take.
The time it takes, when communicating with other Earthlings, is 1,000,000 Earth Years. When you call your buddy in the Andromeda Galaxy be sure to let him know it will appear to take one year less than what he's calculating. All remote observers measurements will be incorrect until you convert it's equivalence to both Earth Years and Earth's location (frame of reference).
2 Observers, 2 different measurements, but once all factors are accounted for you are simply describing the EXACT SAME LENGTH OF THE EXACT SAME PASSAGE OF TIME before entering it in the calculations.
That make better sense?