While there's almost no real difference in the gears either will yield (2.5% or so) it can make a difference. Not in the low gear because 2.5% won't make or break anything, but it can affect the spread of the middle gears. Typical steps in a 9 or 10s are between 6 & 10% or so. If you get a gear chart, compare the ratios yielded by both inners, and compare them to the outer's ratios.
One may yield a gear progression about 1/2 step between those with the outer, while the other may be very close to duplicating them. So with one you get a nice batch of very closely spaced mid ratios (those that work well with either chainring) while with the other you don't.

Not a big deal, but if you've ever been on a shallow grade, or working a headwind and wished you had a gear between the 15 an 16, you'll be happy you could find one using the other chainring.