The only way I've found so far is to put items in the mission that normally the player wouldn't encounter until a certain level. Such as: Terran Empire (Mirror Universe Federation) enemies limits the mission to level 31 and above, Gamma Orionis doors limit the missions to levels that can access Gamma Orionis, etc...
EDIT: This isn't to say that you can't just put in some regular Klingons with a Terran Empire skin to have Mirror Universe enemies at a lower level
So how do you turn your testing character into a maxed out character?
Go to the Create Content tab and pick one of your Test Characters instead of clicking create content. This takes them into STO where you can play the game for a few hundred hours doing Defend the Sector grinding to level up to VA. Then you can test your Foundry missions with a VA character.
That's the only way at the moment, but they will be adding in the feature to level up a character artificially soon. But there is no way to level a character back down again, so be prepared to delete your test characters regularly if you want to test multiple levels.