I know there are images of P-38s on finals with everything down and naturally as combat flaps they would be deployed.
I've also seen museum displays with everything down, curiously, as I wasn't aware that hydraulics were lost when the plane was idle, so don't know why museums display them deployed apart from adding a dynamic display quality.
A great number of other photos of machines in maintenance etc show the control surfaces in neutral positions, which seem to be most common.
Trumpeter provided metal hinges and pins, not to everyone's liking as they are a little difficult to work with. I found that the inner flaps were more naturally deployed down. The outboard control surfaces, however, were more problematic, where the tight fit of styrene and metal near the tapering wingtip halves led to a snug fit indeed.
On the model displayed here, the outer units can be pressed down a little as deployed, but the 'springback' element of tension drew them virtually back to a neutral position. I seem to recall that the instructions were not decisive in display deployment (I'm not at home at the moment, so can't doublecheck the instructions in my files.), but I think as a presentation of the Lightning as a type the model still works well.
I think if it was an RC model and was expected to undertake airborne maneuvers I would be more circumspect in my views, but as I'm not a modeller who requires the exact number of rivets in the 1:1 machine to be committed to memory before building the styrene example in 1/32, and while I'm sure you're correct on this point of technical evaluation, I suspect that the license taken here is acceptable to most modellers.
Happy modelling!