I can't imagine using a transpose function to change keys. I use different voicings in different keys. If I was in a band that tuned their guitars down a half step I would probably do it just so that our chord charts would all match and the voicing so wouldn't be that different. That and I am pretty good at reading the chords off the guitar players left hand since I play guitar as well.
It really isn't that hard to play in different keys. First, you mostly just do guitar keys anyway: G, E, A, D. If it's a jazz band with brass you can add a few flat keys like F, Bb, Eb and Ab. Heck most songs are just four chords anyway: 1, 4, 5 and 6.
Then there are some simple rules for the harder keys. The most black keys any key is going to have is five. With the keys where you use all five black keys, it is just a matter of which of the two white keys that are together do you use.
Key of B: it's E and B (the two lower ones). In C# it's F and C (the two higher ones). In F# it's F and B (the higher one under the group of three black keys and the lower one under the group of two black keys). Mess around with it for a few hours a couple of days in a row and you'll have it forever.
The biggest thing I have against using the transpose function though is what it does to your voicings. Transpose up and key of C voicings are going to have a your chords high and shrill. Transpose down and they're going to be really muddy. I suppose you could learn to adjust your inversions and voice things differently as you transpose up or down, but that sounds like as much work as learning to just play in the different keys.
Plus, what are you going to do if you run into a real piano or organ? What about multiple keyboards? Do you transpose them all? What if you're playing bass parts? They're not going to sound like bass parts if they get transposed out of the correct range.
I really don't see how this is an issue.