Better to build in an option to strip this information automatically. TileCutter should already export as a 24bit PNG, ignoring the alpha channel during composition. I'll have to check this. I'll make it check if the image has an alpha channel, and if so whether that channel contains any data. If it does, I can prompt the user to flatten the image to 24bit (with maybe a selectable colour). If not the alpha channel can be safely discarded.
I'll put it on the roadmap for 0.6.