1) AFAIK the case is the same, apart one has the window and the other does not. There's two color versions but they differ only in the silver front trim (the stripes that run along the optical bays): one (mine) has them in dark silver, another in polished black.
2) The 3x bottom HDD cages are totally made by me, and placed in the place originally intended for a 360-420 radiator. I took three Lian-li EX-H34B 4-in-3 cages and removed the cage frame itself (rear Pcb and rails) from the optical bays mount (5¼ holes and front door). It can be easily done, since Lian-li cages are built with screws and can be easily dismantled. Then I mounted them to two aluminum bars that act as a support bar then bolted to the rad grille. When I'll re-attach all pics you'll see how I made them.
3) The Elysium up front is much like the good old CM Stacker-01: it has 12x5¼" standard bays that are fully usable since buttons and ports are on the top (the CM used up one bay for this, without modding). So you can place any kind of hot-swap module, from 4x2½" in a single 5¼" to 5x3½" in 3x5¼".
4) That depends on your modding abilities.
with no opticals:
4.1) Using my 3 internal cages and 4x modified Lian-li EX-H34B cages up front, shortened with ½" thick fan like I did: 28x3½"
4.2) Front bays with 4-in-3 modules: 16x3½"
4.3) Front bays with 5-in-3 modules: 20x3½"
4.4) Front bays with 4-in-1 or 8-in-2 modules: 48x2½"
The Elysium comes standard with two 4-in-3 internal 3½" cages, not hot-swappable, with a 120 fan. They're fairly standard quality, separately they're available for about $15-20.
I know the silver cages don't match the case main color, but in modding I'm first for function, only then appearance
. A version of the EX-H34 is available in all-black, EX-H34SX but it costs a lot (SAS support) and has no holes on the sides which I needed.