Actually, to me it seems that difference is too broad to be useful; I am not sure word-difference is useful too. At least the latter seems to suggest it applies to words, but in both the cases, they are not defining exactly what difference the tags are for.
word-choice is much more useful, IMO, since it says the question is about which word should be used in a specific context; in other words, it specifies to which difference the OP is interested.
It looks like there isn't enough interest in the merge to do it or kill it, so we'll just keep things the way they are.
The description of word-difference is:
For questions about differences in meaning or use between related words or words with similar meanings.
The description of difference is:
This tag is for questions about the difference in meaning between certain words, or phrases.
I think we should rewrite the description of the difference tag to be:
For questions about differences in meaning or usage between words or phrases with similar meanings.