Could you help me interpret why are the p-values from my PERMANOVA overall results different from the pairwise results if the test statistic is the same?

Hi!
Actually, since you have only 2 levels in chosen column, it is not necessary to run PERMANOVA in pairwise mode, though it not incorrect either. P-value in the upper table is P-value of omnibus test, which tests if there is a variation among all levels in the column. With only 2 levels, as in your case, you can report this P-value and ignore second table, in which each level is compared with each othet level. In that case p-values are FDR corrected and converted to q-values. They are equal between each other just bacause with 2 levels there is no correction needed. P-values from first and second table are different because PERMANOVA will yield slightly different results when running several times.