Hello!
If you first rarefied the feature table and then calculated Shannon, then you can use the same rarefied table for other metrics.
If you run core-metrics plugin within the qiime2, then you need to provide unrarefied table and indicate the sampling depth, so it will rarefy the table first and then calculate alpha and beta diversity metrics.
You also may take a look at qiime2-boots plugin that can perform bootstrapping instead.
Best,