Some difference using --kingdom option

[ZeWLi]

Dear developer,

I used prokka to annotate metagenomic assembled contigs to find the ribosomal proteins. I tried --kingdom Bacteria and --kingdom Archaea options, and I noticed the .fna files were the same in 2 runs. Then I checked .tsv files, I found that some genes were annotated to different annotations (i.e. different type of ribosomal proteins). So I wonder

1. Why this happened, and can I confidently claim the ribosomal proteins are bacterial/archaeal type?
2. Why I also noticed the run using--kingdom Archaea generated far more ribosomal proteins than the run using --kingdom Bacteria?

Regards,
Edwin