I think these are tag synonyms:
They basically do the same thing, but not mean the same thing. You get the difference through comparison. I think they should be tag synonyms.
Certainly, I think some of the questions tagged difference should have been tagged comparison, but they serve different purposes; as a first thought, comparison can actually refer to questions about words that refer to comparison.
However, as it is, the tag descriptions are unclear, and perhaps we should be editing the questions to identify those that should have difference tags instead. It really depends on the perspective, but they're not the same thing in the end; maybe just a tag description edit will suffice.
On the other hand, there are so few questions tagged comparison anyway, so just quickly, I think there are only a couple of questions I can find where it wouldn't be appropriate to re-tag as difference:
I'll leave it to the mods and the community, though, but I don't think they're synonymous.
I think we've got something of a use–mention distinction here. We need to distinguish...
1: questions asking for the difference between two or more alternative ways of expressing something
2: questions about usages involving comparison (e.g. - metaphors, similes)
3: questions about the use of comparatives and superlatives (such as better, worst)
Personally, I'd be in favour of using the above highlighted words for those particular senses So far as I'm concerned, the (currently, 31) existing instances of comparison should thus be re-tagged difference.