As I just wrote something in another thread about a proposed -100 penalty [webmasterworld.com] that I feel apploes to your question as well.
Yes, the same site can have different degrees of penalty for different keywords and pages. Today's penalties are not necessarily calculated by substracting a number of positions. Instead, consider these possibilities that are all mentioned in one or more Google-owned patents.
The final ranking/relevance score for a url has several components. Some depend on the query terms and some, such as PR, are "query-independent." Just one component can be lowered by some number, or multiplied by some percentage -- then the final SERP is shuffled via what we can call a re-ranking.
Or more than one component may be affected by a subtraction or multiplication - or even a total zeroing out. Then it's also true that the final "composite" ranking can also just be subjected to a subtraction or multiplication.
So a lot of the time it's not going to fruitful to try to pinpoint a penalty "number" and use that to try to get the penalty removed.