I don't use mechanics or rules for non-humans until I really need to generate them and that is well after they are introduced to the team. The story as it evolves generally leads to what powers are needed by the concept and the character interaction. For humans I tend to stay pretty straight within the bounds of "mundane" and add odd stuff rarely.
So the rules are really for the players in my games. Even then we hand wave a fair amount of things which are not thematic to goals too.
I think it is important for a SG to stay witin the bounds of the rules, unless there is a really good reason. As a player I'd hate to to face an NPC who obviously is "cheating".
That being said I certainly don't stat out fully all NPCs I use. i have a pretty good idea of what they should be able to, and if they are important enough I'll stat the full character.
At some point I sent a conflict seeking Flambeau maga on my players. I think their magi had asked for it, they stole something mildly related to her and she took offense. The player magi were just post-gauntlet and i knew they were not very dangerous. So I only sent this one maga and envisioned her within 5 years of gauntlet. I improvised what spells she used and her apporximate casting totals, but Penetration realy wasn't an issue as none of the player magi had Parma Magica at that point. However my vision of what magic she used changed during the altercation, and she did seem almost too broadly skilled.
During, or afterwards, it was discusses as to whether this particular maga was feasible. Naturally I took this as a personal challenge and built her in MC. As my initial vision was different from wha she turned out to be I gave her all the spells she had actually used, instead of the ones I wanted her to have from the start. But I had little difficulty in designing this maga.
So in conclusion: Apparently I can wing it just fine, within the boundaries of the rules. Which is why I don't often design NPCs with full stats, or even any at all.
However, is it cheating if the storyguide uses rules entirely from outside of the set RAW mechanics to represent both the player and the characters complete lack of knowledge about the enemy they face? So if the antagonist is from some mountain in Ethiopia wielding magic and powers the players have never see or experienced, why should you not completely fictionalize the methods of that beings power? This is done for two reasons. First, in character, the being is not Hermetic and so, as long as the being remain internally consistent with the set of rules that the SG created for that being, then it should only be the PC's who don't see the world as fair.
Second, and this is where there is some ambiguity, when dealing with any RPG you often suffer from out of character knowledge worming its way in. Some players filter so well they often hurt the story just to not appear to "cheat" while other players scour books and their notes and can come up with almost any solution to any problem you throw at them. And so even if your villain is one of the greatest antagonist of all time, they will still over come them in 27 seconds. 
So as the SG, I will, when dealing with a villain that uses a system or power that the characters have NO Lore or knowledge of, something that is truly alien to them, I will use a different game system entirely from the many independent sources I have played. I stay within those rules for the NPC, and allow the players to figure out the villain for themselves.
Of course as soon as they do figure it out and start to grasp what they are dealing with, I will switch to expressing the villain in Ars Magica terms, signifying the return to wisdom and understanding the being they face. I guess it is metagaming at its highest point. But it is effect in making the footing equal for all players and not rewarding the one player who has all the books and has played for twenty years, over the newbie who is smart but has two books and has played for two years.
There is no problem with using your own mechanics. But, IMO, they still need to obey the general mechanics.
For example, a supernatural power should be subject to analysis by InVi (even if it is difficult), a supernatural power should be possible to dispell by PeVi (even if difficult), and a supernatural power needs to generate a Penetration Total to overcome Magic Resistance, and be affected by aura, etc. Breaking these sorts of rules is unfair, because it breaks the player's expectations of what the player characters can do and how the game world works. Even so, it's OK to occasionally break these rules (for example, even in RAW, demon powers are sometimes not subject to InVi analysis). But, if you break these basic conventions that is the story. I think it is lame if every (or even most) "enemy characters" break these kinds of rules; you may as well not be playing ArM.
I can see that is a reason to mix things up. On the other hand, I don't usually bother.
Personally, I have come to conclusion that, as storyguide, trying to prevent player knowledge impinging on play is pointless. Afterall, the game only makes sense in the context of player knowledge. For me, how to deal with player knowledge is a player decision. I don't really know what the individual players know or don't know, and there seems to be little point trying to endlessly out-guess the players. It is up to them to decide how to use their knowledge. Does the character do what the player thinks to be the best course of action, does the character do what the player thinks to be a hopeless course of action? The decision really comes down to the type of story that player wants to tell.