In the newest version of BnB (1.1.3), there is no longer electric gas around invader portals. But either way, gases can be collected. You just need a gas collector, a gas tank, and possibly some gas pipes. I think somebody said that electrical gas can't be collected though. Even if it could, it probably wouldn't be worth it. As the gas doesn't flow, you'd have to place the collector right next to the block you wish to collect, and would probably be fried before you got a chance to do so.
Steel and hepatzion will not break ardite. When boosted they go from bronze to steel, and I belive that ardite requires shadow steel (again, based on v1.1.3).
Is your base around the server spawn point? Minecraft keeps a 16x16 chunk area around spawn loaded at all times (personally I find it kinda annoying). As far as mobs spawning and pilling up like that... that doesn't seem right.
I've heard of the portal issue. Unfortunately I think it's a side effect of the fact that roguelike dungeons have all kinds of open space in them, and the way that minecraft checks for and creates portals. When you create a portal to the nether, the game finds the closest place that corresponds to where you placed in in the overworld that it can actually put a portal. Sometimes it's a little bit farther away. Then when you come back, the game looks for a portal within a specific range to the spot in the overworld that corresponds to where you are in the nether. If it doesn't find one within that set range, it will go ahead and create one in a viable spot. Or if there is no viable spot, it will keep searching outward. But as there is a ton of space in the dungeons, it can find a viable spot.
So by creating your portal up in the sky, the portal in the nether isn't able to be placed up that high and has to be down lower. When you come back, your portal in the sky is not within the normal range, so instead it creates a new one.