Thinking about EE3, im suggesting that EE3 Energy should only be gained from very limited resources (maybe even only from an item you only get through dark energy?), but that it can be spend on most things. It is still very nice not haveing to hoard wool or similar, so i wouldn't remove EE3 entirely.
Yeah, unfortunately as far as I can tell, EE3 doesn't let you designate items as 'break for points only' or 'purchase with points only'. Anything that has an EE3 value can be broken down...And you can't build anything that doesn't have an EE3 value.
It's a kind of a broken mod. It encourages laziness. I used it to replicate a ton of chicken feathers and smooth stone for when I was building my towers (I use holystone). Also a ton of obsidian. But unless I am in a hurry (like I can't find something when I'm recording an LP) I try to avoid using it for 'real' resources.
Just my thing. YMMV.