Solarius : Even in vanilla UFO, the setup time of heavier weapons is already taken into account (and game-balanced) by the high TU% cost.
Remember that if a unit has enough time to move, fire, and move again in same turn, the character is actually shooting while running.
So if you're really serious about modeling real-world weapons which are normally fired from a static position (sniper rifle with biped, machine guns), first you should set up the firing time to 100% TU. Then, you'll see you don't even need a special case about crouching : You plan your move so that you end up in the right place, right angle, and crouched. This is the "normal" firing stance, and weapon accuracy is designed for it (ie. sniper rifle : 125%. 150% or beyond is ultra-OP) . If you're 4 TU short, you'll skip the crouch : the unit will be able to shoot anyway, with this slight penalty which mimics the "hurried-ness", and it's good.
And flying units can not crouch in air, so they have the mandatory -13% malus (/115%), it makes sense (no stable support) and counter-balances the OP-ness of air superiority.