Is the primary reason most people mount their boards on top of their pods is ease of access? It would seem to me that internal mounting would be better for protecting the “brains”.
I mount electronics on the middle deck of my rover rather than the top. I guess that could be considered somewhat internal.
8-Dale
Yes, the mounting location is for ease of access. In some cases, depending on the design, you may have no choice as to the “ideal” location. Such limitations include lead lengths such as the length of servo wires as one example.
You can mount your tronix anywhere it will fit. There are no rules that say you must always mount it for easy access. For most people though, we are always fiddling and tinkering and it would be a pain in the *** to have to dig it out every time you want to change something. 
I go through a bit of this because of the fact I mount my electronics on the middle deck instead of the top deck. I have to remove the top deck, which is very easy to do, to get to the electronics. This is not a problem right now, because I don’t have anything mounted on the top deck (yet). This will change in the future though.
I also mount my electronics on the middle deck because it makes it more difficult for my cat to get to anything. She thinks W.A.L.T.E.R. is her favorite cat toy…
8-Dale
I filled up the innards, then moved to the top deck when I ran out of space! When placing bits on the inside, carefully consider where connectors will end up so that you might get access to them between the legs rather than opening it all up.