Yep, those are options. As are a dozen or so more configurations you could dream up. With benchwork like that underneath, you don't need any additional support under foam panels, but it's not WRONG to put plywood under the foam if you wish. Some people like having a solid base to put screws into, but it's not necessary.
Similarly, if you want lots of terrain relief below track level, you could make your base 1" foam panels, and build up layers of 2" foam over it. If you're planning to use under-the-table switch machines (servos, Tortoises, whatever), thick foam bases mean you need to plan for your motors a little, but it's not too hard.
Your roadbed can be either foam (rubber) or cork. I wouldn't paint until everything is in place, but again, it's not wrong to do it the other way either.
There is more than one right way to build a layout. You just do what seems right, and fits within your budget and schedule.