Hi Lucas,
I don’t have a strong opinion and the GTDB reference trees should be treated as effectively unrooted. You might find the following manuscripts useful:
Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution
https://academic.oup.com/ismej/article/18/1/wrae129/7713227
A rooted phylogeny resolves early bacterial evolution
https://www.science.org/doi/10.1126/science.abe0511
Cheers,
Donovan