Thanks!
As discussed in that thread, the PERMANOVA is performed first to look for differences between groups and give you a p-value of significance.
Afterwards, the box plots are made, and if that p-value is under your alpha threshold, then you can look to see what groups are most different. I think of the box plots as a post-hoc test.
Yeah, the difference are very small but I can see a few...
Pristine to pristine: slightly lower mean, some outliers, larger standard deviation
Human to pristine: slightly higher mean, no outliers, smaller standard deviation
Remember that a stat test can be significant, but the effect size can still be very small.
Paper: Using Effect Size—or Why the P Value Is Not Enough - PMC
Interactive visualization! 
https://rpsychologist.com/pvalue/
When you view all your samples in a PCoA plot, do these groups visually overlap? The file core-metrics-results/jaccard_emperor.qzv should contain this graph. I posted about how I read those graphs over here.
Let me know what you find!
They are just two different ways of calculating how different two samples are.
Jaccard is the percent of taxa not shared by two samples (A+B/union in the diagram below)
Jaccard and Bray are similar methods, so it makes sense to me that your graphs are similar.
