On the UNION tool, allow for deselecting columns that aren't relevant. Leave the union exactly as it is, and you could go into the manual configuration. Align the columns just as you would in the manual configuration. The addition would be that you have the behavior like you see in a join tool where you could deselect C1, C2, C3.... Cx.
Too many times I have a union and there are fields I simply don't even want to bring in, but then have to add a select tool right after in order to remove them.