Good one! I've seen it done once, coincidentally with a Phantom, in 1/48th scale.
The model was posed nose up, with the nose gear leg at full extension,nose wheels just off the 'deck'. The afterburner effect had been created in a similar method to the way you described. It appeared tp be two 'tubes' of clear film, plastic or 'Cellophane', one inserted into each jet pipe, probably about two inches long, maybe a touch more. From what I could make out, these clear 'tubes' had been airbrushed with transparent colours, in reds and yellows, in a graduated effect. It actually looked quite convincing from certain angles.
However, there can often be a problem trying to model any form of 'moving' item, such as smoke, flame, water etc, as the movement depicted can only physically be for that moment in time, for obvious reasons. Smoke, for example, will evolve, spread and dissipate, something which is impossible to re-create in a static representation. On the other hand, these effects (on models) can look superb in photographs, although digital imaging and facilities such as 'Photoshop' have, to an extent, rendered such techniques redundant for photo or other imaging purposes.