I don't agree with you at all. You say you have to use these perks, opinion. You say LEP is too large, opinion. I am stating that approval bonuses are not calculated properly, and that can be exhibited with the simple fact that higher tech buildings are far less useful than low tech buildings.
The only reason why higher tech buildings are less useful than lower tech ones is due to LEP. Again. Nothing else is subtracted from morale; everything else that comes off it is either a % or a divisor. LEP would actually work better if it were made into a % penalty (which I believe it was at one point in beta), since then it would stack with all the other %. Hence, I don't think it's a bug. It's a direct result of an intended change. And yes, it turns out that change was a bad decision, but it's one that's quite easily reversed.
Morale works as a concept. All the % bonus buildings become useful again as long as base morale never goes below 1, and the only mechanic in the game which can cause that is LEP. Hence, it's LEP mechanic that's broken, not the approval mechanic. The penalty works when we're just using morale to limit tall-ness, and ca be countered (possibly too effectively considering the population limit).