you know i still dont get this 1 lightyear is just shy of 6 trillion miles why would you ever want to make a trip take 60,000 times longer?
I would call that a typo in the gal civ 2 database. Switch out 10 million to be 10 trillion and then it is better, but only slightly
While it is more common for the statement "A seems like B" to use B as the baseline scale, it isn't entirely wrong to use A as the baseline scale. It's unusual and not common practice (and is in fact the opposite of common practice) and therefore confusing, but not exactly wrong.
Also, if you don't know that a light-year is five point something trillion miles, you might not know that 10 million miles (which sounds like a large distance because it has a big number in it) is a shorter distance than one light-year (which sounds like a small distance because it's 'only' one light-year). Mixing units, especially units which people don't use every day or which are not commonly used to measure the same things (and yes, I know that both light-years and miles measure distance, but you're not likely to measure the spacing of stars in miles, and there's not much reason to use light-years on a smaller distance scale), is an easy way to obscure which is bigger, and the less likely it is for someone to know the conversion or even the approximate relative magnitude of the units in question, the easier it is to become confused. I would expect that most people would be able to tell me instantly that a light-year is 'bigger' than a mile or even a few thousand miles. Whether or not they'd be able to tell me if a light-year was larger than 1 million miles without having to look up just how big a light-year is is another question entirely.
Regardless, the statement in the manual makes at least half of its point abundantly clear - both trips take about the same amount of time, despite being significantly different in total distance traveled. It might not be entirely clear from the specific statement that you really ought to be using the 10 million mile trip as the probable baseline travel time, but common sense says that if you're using a piece of technology to reduce travel times, then the shorter travel time in such a statement is likely the baseline.
I will also point out that we are not necessarily guaranteed that the ten million mile trip was actually the trip of lower duration. After all, the stargates, which are described as being a (slower) form of hyperdrive that was only able to send ships between any two stargates, predated the hyperdrive, and given that stargates were supposedly massively expensive structures, it's entirely possible, and in my opinion probable, that there would only be one stargate per inhabited system. Since it makes a fair amount of sense to use light-years in measuring the distances between star systems, but not much sense to use light-years to measure the distances within a star system, there's a reasonable argument that a trip of a light-year or two would be interpreted by a person within the game universe as taking less time than a trip of a few million miles, as the first implies intersystem (and therefore stargate) travel, while the second implies intrasystem (and therefore standard sublight drive) travel.
If an average home system for a species sufficiently advanced to have a form of hyperdrive is similar to our own system, then there are potentially interesting objects within the system at least ~3 billion miles distant from the homeworld; without hyperdrive or an intrasystem stargate network, such journeys would need to be made using whatever the subluminal drives are or were. I will nevertheless grant that hyperdrives do not appear to be capable of superluminal intrasystem travel, under the assumption that each move action represents a roughly equal period of time, as it takes a minimum of two move actions to move from Earth to the Sun in a GCII/III game. Since each turn represents 1 week of time (at least in GCII, not sure about GCIII but I don't see why that would have been changed), you would need to be capable of about 2400 move actions per turn before you could say that a hyperdrive-equiped vessel was capable of matching the speed of light between Earth and the Sun; if the comparison is to use the distance between Earth and Jupiter, then you'd require about 460 move actions per turn before hyperdrive attains lightspeed on that journey if Earth and Jupiter are separated by only one tile. Regardless, even with much lower numbers of move actions per turn, movement within a system using hyperdrive is still very fast, being on the order of tens of hours to a couple days (with the 3 base moves of GCII ships, up to a maximum of about two weeks for intrasystem travel, at least between the system features displayed on the map), and still likely faster than whatever the standard subluminal drives are capable of doing.