I don't really know how big a deal this is and i'm undecided on the whole issue. Generally, when a developer is moving away from a title to focus on the next project, it makes sense to encourage the community to modify the game, as long as it's done with a good purpose. That's the problem here, ensuring that modding will not be used to exploit and cheat.
It's not as if they are modifying something that will receive any new expansions and patches, but the aim should be to make the game last longer, not turn it into a bunch of cheats that will drive everyone away.
As an example, take a look at another of Ubisoft's series, Silent Hunter 3 and 4. There is a very active modding community there and the best mods get compiled into super-mods that totally turn a 3 or 5 year old game around and make it worth playing for a couple of years more. People who worked with Oleg have worked on some of the mods and the results, at least in the visual departent, are stunning. I saw some screenshots of a 190 cockpit with higher resolution textures and it was like i was sitting in one in a museum.
I think Oleg knows this and that's why they already said they plan to increase 3rd party support for BoB. Why? Well, it's very simple. Even if your game stops being the best, there will be people who will keep it among the best in its category for free. Then, when someone for example wants to play the Grey Wolves Expansion pack, he will have to buy Silent Hunter 3 and the developers still get money from one of their older games, money that funds their next project. Everyone wins.
In the end, i think the attitude towards the IL2 modders is negative because they started doing it while IL2 is still awaiting a final patch. Oleg and team are striving for accuracy and they are rightfully worried that if loopholes are discovered, accuracy might get compromised.
However, i'm sure they see the benefits of a modding community and i guess they'll make BoB modable in a way that ensures it's not exploitable. I think that's their main issue, IL2 is essentially a "closed off" product, so to mod it you need to essentially "hack" it. If it was a product open to modding, people would not have to look for ways to "hack" it because they would have tools provided to them, hence there would be less danger of using the knowledge of the code for malicious purposes like cheating. If people can make the game they love better, without hacking it, then they'll have no reason to delve into the darker aspects of manipulating the code
For me, the best thing would be to have a detailed physics/world/game engine that will be able to "sense" an object in the game world and calculate the flight/damage model on its own. For example, let's say i model a spitfire Mkv in a 3d suite to make a channel front addon. I would then use a tool provided by the game (let's call it a properties calculator) that will calculate the damage and flight model, according to the 3d object i load in it and the rules of the game engine.
Everyone will be able to load my Spit MkV in the properties calculator and see if it's accurate, so i can't cheat. If i give my favorite ride a 500HP non-historical advantage, other players will be able to see it and call me out on it. This way, people can add new things into the game, but the game engine reigns supreme over the properties of each object added.
Of course, this sounds like a lot of work and it probably is, but it's the only way i can think of that will allow seamless integration of new accurate/historical content into the game without the need for constant coordination with the developer team. Imagine for example if we could tell the properties calculator what kind of material is used on every part of the plane. You would load your 3d model in it, mark/select areas of the airframe and select the materials from a drop down menu, let's say aluminum alloys for wing spars, fabric covering for ailerons, steel for armor plates and so on.