PCB design for intrinsically safe equipment to 60079-11 standard
What is important to realize is that the distances are necessary only if the intrinsic safety will be compromised by a short circuit (that is the failure model, if you don't have the distance you must assume a short circuit between the lines).

As you design your device your concept should be aware of that and your ICs should be in an area where the intrinsic safety will be held up even if a short circuit occurs. That way there is no distance requirement anymore and you can use BGAs and other fine pitched devices.

The same holds true for the PCB stack. In critical areas you have to have those distances but in protected areas you can get as close as you want. Layer to layer separation falls under "Separation distance through solid insulation", so no special rule is applied there.

I'm not an authority in the field and can give you only the recommendation to involve your certification inspector early in the process and talk through your concept before doing major work on it. We had some serious changes in our circuits because of our concept not matching what was expected and misunderstandings of the standard.