There's a range of options for dealing with this (none of them that authentic!).
Above general volume controls, some 'instruments' have 'voicing' parameters which extend at least to amplitude, per rank (and hopefully per note), which allows some control but can also create micro-tubas etc.
Manufacturers also sometimes provide a volume pedal to the Great, but not in the manner of 'enclosing' the department, as the attenuation of higher frequencies is not simulated (- scale becomes quite confused.)
Another possible option is compressor/limiter devices, which are used in Public Address and sound recording to control the dynamic range of audio signals.
It's all fairly unpipelike, which isn't necessarily bad (e.g. I find it fairly easy to believe that the swell-box was invented to controll volume but not brightness of sound), but with our organ expectations, I guess the point is that these 'flight simulators' are ok for practice, but if you must have an electronic for preformance, go for custom-built Copeman Hart, Phoenix, etc.