I think the official answer is no because Cryptic is a bit uneasy about Foundry authors making their NPCs too weak and therefore exploit missions.
I'm not sure how, though. Consider: The points & loot drops of enemies is directly tied to their strength. So if all the enemies on a mission are nerfed into helplessness, the rewards for defeating would likewise drop to nothing.
Second, the repeatable daily mission to do three Foundry missions is already exploitable. People can, and have, made plenty of missions that contain no enemies at all. Tutorials, fleet meeting rooms, even dance clubs and other purely decorative maps exist. As soon as players spawn in the mission is complete. Moreso, it still counts as doing a completed mission for the quota, and thus allows quick & easy rewards to those trying to get their daily three in for that task.
That being said, so long as Cryptic bothers to make sure that their difficulty/reward algorithm is working right, I can see no reason why they should not allow fully customizable foes in the Foundry. In fact, it would actually reduce the amount of exploiting already available.
It would have to be incorporated into the system code at some point I'd think for Neverwinter. Boss battles and such DMs have been modifying the standard monsters and levelinng them up since the game started so the tech for it would have to be implemented at some point.
That is, can you make an enemy contact Level 5, and then roll in with your Vice Admiral and sweep the floor?
I want to make a set of missions for people who want to fly their Tier 1 starships at Vice Admiral rank; the requirement then is for the baddies to be made weak enough for a Miranda to take down, and the only way to do that is to lower the enemy NPC's level.
I think what the original poster was going for here was, will we ever have the ability to modify the types of weapons and tactics used against us. For example, every Cardassian Galor-class uses feedback pulse. It would be refreshing to go up against a Cardassian Galor-class that suddenly slapped on a tractor beam and then began releasing mines. And if you're encountering a fleet, the ships would not be using carbon copy tactics.
Or say you're rescuing a Starfleet Officer from a Romulan prison camp and you'd like the NPC Strafleet prisoner to carry a stolen romulan disruptor as opposed to a shiney federation phaser rifle.
It's not so much a question of making the enemies weaker as it is just having the ability to vary their attack profiles.