That depends on what you mean to "cross-over comparisons."
As this site is a Q&A site, and not an open-ended discussion site, questions here should be the kind of question that has a "right" answer. Ideally, that right answer should come from a canon source, or at least something vaguely authoritative. We want to make sure that, if someone comes up with an answer, it's possible for the person asking the question to "know" if it's right or not.
For example, if you asked "Could Force Lightning hurt Superman?", that would be an impossible question to ask, because there is no point of reference. We could speculate over whether Force Lightning qualified as magic in the DC-Universe-sense, but that's all it would be: speculation. And we don't want speculative answers. Alternatively, if you asked something like "Could the Death Star beat up a Borg Cube?", the answers you get would mostly be opinions: "I think the Death Star would win because _____". And we also don't like subjective or opinion answers.
On the other hand, a question like "Could Hulk beat up Superman" very well could have a real answer, because those two canons have interacted before. In that case, the person asking the question would be expected to specify that -- indicate that they're looking for a situation where Hulk really did fight Superman and what happened.
So, it's not so much that we don't like cross-over questions, it's that we don't like purely hypothetical or purely subjective questions. The cross-canon comparison questions are just an example of the kind of question that usually falls into one of those two categories.