This means that the machine will automatically output items from the bottom,
but items can be pulled out by item pipes from the right,
and it will pull fluids from tanks above, but they can be pumped in the left.
This cannot be changed (on any GT6 machine).
I think covers blocking still happen in some cases. The one I can remember is I tried to put a redstone controller cover on the igniting side of an igniter and that caused it to stop emitting ignitions.
No, Covers do NOT block things, they do the exact thing they are supposed to do and nothing else. What you might have forgotten in your Setup is that the Controller Cover takes control of the Igniter like it should, and that you need to send a Redstone signal into that specific Cover in order for it to actually do its work.
I somewhat remember weird things happening when I attached two identical covers to a single machine. Not sure which one actually worked. They were redstone-control related.
I hope I’m not confusing this with an issue of attaching “Automatic Machine Switch” covers - 1 to polarizer and 1 to electromagnetic separator. One Machine is above electromagnet, one is below. Doesn’t really work.