It is an a priori issue. Speak slowly when you debate about it. To win, the negative needs a clear interpretation, that the affirmative doesn't meet, that is better than the affirmative's interpretation. If the best policy includes the entire plan, I'll vote aff. Legitimate permutations include the entire plan plus all or part of the counterplan and nothing else.
Topical counterplans are almost always legitimate.
Conditionality is not indefensible. I'm often not certain what exactly the permutation is. Debaters talk fast. There is almost an hour from the end of 2AC until the end of the round. I have a bad memory.