The roof needs to be either reactor glass or reactor casing. And you definitely can fill spots - you can either fill in most of the roof and place the fluid "against" the underside of the blocks, or fill in with a bit of cobble and place against that, then remove it. Remember that because liquid Ender flows down (and because you don't need source blocks, flowing is fine), you only need to place the top layer!
It is air, but you can fill it with anything, glass or whatever, as it doesn't matter. It doesn't make a difference if the liquid Ender spills within the reactor either! And here's why: because of the way the mechanics work, the mod ONLY takes the blocks directly to north, south, east or west of the fuel rod blocks into account! Diagonals don't matter to a given fuel rod.
Yep! Well, not for free - the bigger reactor casing costs more resources
but that aside, yes - more RF for the same fuel rods.