Monogram Close-Up doesn't really elaborate all that much on planned operational variants of the Kikka, focusing heavily on the development history of the prototype instead.
The book, Japanese Secret Projects: Experimental Aircraft of the IJA & IJN 1939-1945 by Edwin Dyer, while also giving good information on the development history of the Kikka, also gives more information regarding the different planned operational variants of the Kikka, which I think is relevant to representing an operational Kikka in IL-2 1946.
According to this book, the specifications you listed are in line with the initial IJN requirements which had the less powerful Ne12 engines in mind.
On page 116, it lists the performance requirements for the aircraft with less powerful Ne12 engines as 513km/h at sea level while carrying a 500kg bomb.
When it was decided to go with the more powerful Ne20 engines instead, the IJN requirements were revised to 620km/h at sea level while carrying a 500kg bomb (page 117).
In the end it is as you said, what the mod maker wants to do with the mod. Since Lone Wolf brought us a properly armed Kikka and a planned twin seat variant. It is apparent to me that he wants to focus on planned operational variants of the Kikka. Otherwise we might as well fly an unarmed prototype, which would not be of much use in a WW2 air combat game.