I don't quite understand that comment, alignment of what levels? What is your system, what levels could we be talking about? Of course LDA underestimates the band gap (and perhaps also HOMO-LUMO gaps in molecules), and there are ways to adjust for this, but not by just "corrections", rather you can use methods like LDA+U or MGGA (or even HSE), but that's a different story, then you have to re-run all simulations. The key point is, in my opinion, that if any of your conclusions critically depend on the "level alignment" - whatever it means - then it's best to check if it's an artifact of LDA, or the same would happen regardless if the band gap or HOMO-LUMO gap was corrected.
