You also have to understand that there are just some pits out there that aren't conducive to armor shielding, i.e. the larger Sal Kar pits and the super heavy Morskoj ones.
You can mount a genny either directly over or under the pit, use an Isba spacer or equivalent and point it forward, then mount an armor plate in front to cover the pit from direct fire.
There are many ways to cover a pit completely, where there is only a very small gap or even no gap between plates. Spacers aren't the only things to use to help with coverage. A prime example is using the Rih missile counter as a spacer.
Here's a simple example of a covered pit:
- C110/100/20 pit on top of Naqa legs