you can still put lava cans into magmatic engines using hoppers and they land in the depreciated slot instead of filling it, to boot.
Just by the nature of how inventories work, you could use a Hopper to put diamonds in there as well. I could probably throw a quick hack into prevent it - not sure I consider this a bug so much as a quirk.
Honestly, I feel that the wiki does a pretty good job of explaining how to install the mod, and the mod itself is complex enough that people really need to be familiar with the wiki - as incomplete as it is - as well as NEI. I won't say no to an installation video, but I just don't see it as a huge deal myself.
Blulectric Engines work fine with both Cells and Conduits - the graphic issue on the conduits is entirely on Elo's end. You *may* have to temporarily place something else down next to the conduit that the engine is powering in order to change it from blue to orange (and see the change). You can then remove whatever powered device that was and it'll work fine. I believe Elo will be fixing this in the future.
I'll have to think on the Magmatic engine thing - the main point was that I wanted to prevent Cobblestone from being a viable fuel source; that's just too easy.