Assessing beta diversity variations with time
Rather than Mantel, I would suggest doing a procrustes analysis. I didn't know much about it (and still I don't) but a reviewer required it for a paper I submitted, so I used the implementation in vegan package. You can also give a look at this nice tutorial
The idea of procrustes is similar to Mantel's but it should perform better for this case.
I don't what to say about the second question, sorry!