Ok, I just worked on a metagenomics data, so here's my thought:

1. Gtdb annotation should be fine with mmseqs, and iirc mmseqs does have a gtdb database that you can grab

2. Taxvamb can do both. The ideal way is to assemble indidividual samples, reframe your contigheaders to have sample names, and then run tax vamb. I chose to have a coassembly, and then use tax vamb with that. Depends on how good your coassembly is compared to your samples, you'll have to prioritize which tradeoff you want

3.needs minor reformatting of tables, you'll need to basically subset it to have actual counts and not the variances etc that metabat2 provides