The major differences in these mentioned tunes is going to be the maximum allowed timing, based on the octane used, and the firmer shift points for your automatic. If you go with an 87 octane tune, the tunes parameters for timing are going to be set lower in order to prevent detonation. If you have a 87 or 89 octane tune, and use 87 octane fuel, you may get damaging detonation because of the timing parameters, so be sure to use the recommended octane for the tune chosen.
Here's what I'd do: install the 89 octane tune, run the Mustang with it with a few 89 octane tankfulls, have some "fun" sprited driving, then load the 87 octane tune, and use 87 octane fuel and do the same. Judge for yourself with the type of driving you prefer to do, then decide which tune is best for you based on this. It's best to start high (octane and tune), then drop down to a lower octane and tune as to not have to worry about low octane fuel with a high octane tune.
Some folks can have fun with the 87 octane fuel, and save some fuel costs; others will be more "spirited" with an 89 or 91 octane tune and fuel, and will pay the added fuel costs to do so.
Me, I go the route of a 93 octane tune and fuel, as I can get 93 octane in Florida
, and it does indeed wake up the engine that much more. And the added costs for running that fuel are worth it for me.