Hi @C_smith, welcome to :qiime2:!
That is the norm for most dbs, even GreenGenes and GTDB, as chloroplasts evolved from Cyanobacteria, thus it is part of their taxonomy.
Check out the Cyanobacteria and chloroplast wikis too. The same goes for the mitochondria from alphaproteobacteria.
The earlier, deeper taxonomic annotations (i.e. domain, phylum... to class or family) reflect microbial ancestry, where as lower-level / more recent taxonomy labels (class / family down to species) reflect the organelle / plastid of the eukaryote in which they reside.
It seems that ChloroplastDB: the Chloroplast Genome Database might be perfect for your needs. 
-Cheers!
-Mike