http://www.cwgsy.net/private/rick/MH_Airbox_V1_6.pdfWell. I took those pictures and created that Motohooligan installation guide back in the day.
Those are the pictures I took of my bike with me fitting his air-filter!
And I think that there is no gap when I plaited the throttle bodies into position. Although, I admit it is hard to see at the resolution the pictures were taken. But it would have worried me if mine had a gap - and like you I would have mentioned it if it was something that was a concern because I wrote that document for people like me who would be not sure about everything and needed reassurance. So I'm pretty sure there wasn't a gap. But my bike was only two or three month old when I did the mod and maybe the rubbers were more flexible.
So…. thinking about it more, and looking at the picture I took all those years ago…it seems to me that your gap could be attributed to the gap which was taken up by the bottom wall section of the big, plastic air box. Isn't this where the air box would sit and then the throttle bodies are attached from the inside of the air box? Maybe the rubber housing on the throttle bodies has kind of worn/deformed so it only wants to push down as far as it was placed when used with the airbox?
If this is so then you shouldn't worry about it at all because this is the position it was fitted in the factory and the fact that the air box wall is physically missing is irrelevant to the lengths and specs of the workings of the throttle bodies and inlet tract.