You must understand that no 3rd party developer knows much about the exact details of ths sim: nobody even knew it existed before the announcement!
The exact wording of the FAQ is not "most add-ons" but, a more encouraging and encompassing "virtually all add-ons", indicating a very high degree of backward compatibility.
Nobody knows the "few exceptions" they say might have issues, and of course nobody knows what would be required to fix those.
My guess, which is complete speculation, is they surely must have changed a lot the Mission system to add those new features we see in the trailer and, since the Mission system was never completely documented and the included editor simply doesn't work reliably ( as far as I know, those making missions are using a combination of FSX/P3D tools and XML editing by hand ), it's likely anything related to Mission and/or Bush flights might need some reworking, which might difficult or not, depending how much hand-editing was made to the source code by the individual developers. Bush flights are probably easier, since they are usually made with automatic tools that operate by starting on a Flightplan but at this stage it's only a guess work based on very limited information.
Note that, if you read the sentence in the FAQ page carefully, it's made of two separate sentences, with the first one discuss working/not working add-ons in general, and it says that "virtually all" will work, and the second part saying that Marketplace add-ons won't have to be repurchased.
Microsoft surely cannot guarantee anything about upgrade policies on non-Marketplace purchases, if a certain developer decided to charge you for just a new installer, there's nothing they can do about it, they can only comment on Marketplace products, and here they said you will not have to purchase again anything. This is a further indication that, if there is work involved to update something that is not already working as is, it can't be something too complex to do, otherwise they wouldn't be so sure about free updates and they wouldn't said that, it they knew it could possibly take months to convert something.
And of course, if you wanted to know about something more FSDT-related, I can only say that we are fully committed to offering free updates, even for products bought outside of the Marketplace.