I started with that case or one virtually identical to it and sometimes still use it although attachments to the M-Lok side rails of my gun mean it is now a tight fit. I discarded the bottom foam section and replaced it with two layers of 7/8 inch thick Kaizen foam, something pretty much everyone here swears by. I personally prefer working with two layers of thinner foam or a layer of Kaizen foam on top of an existing layer of pick-and-pluck to get a nice tight custom look.
Here is the original version with the gun in place:
And here is the current version:
I have since replaced the Plano with the heavier but still inexpensive case from Harbor Freight shown below:
All of my cases have this sign on them in hopes of deterring casual theft:
See my post above re where to purchase the foam. I have not found any place in the Louisville area that carries it.
Regarding your questions above and as you can see from the photos, two 7/8 inch thick pieces adequately fill the bottom section. You do not need a full two inches as the egg crate top will be compressing and holding everything in place anyway. You just need enough height to make your cutouts to restrict lateral movement.