Where to download confier (pine) or A. thaliana annotated reference RNA transcriptomes in full .gbk (GeneBank) format?
You can download the entire set of annotated RefSeq transcripts for a given genome assembly from NCBI Assembly portal. 


Go to https://www.ncbi.nlm.nih.gov/assembly and search for Arabidopsis thaliana
Use the 'Download' button to pick 'RNA Genbank format' as the file type and 'RefSeq' as source to download all RefSeq RNAs annotated on this assembly in Genbank format. 
 


Note, however, that the RefSeq transcripts in this file will be the ones that were annotated at the time of the release, June 2018, in this particular case. It is possible that additional RefSeqs have been curated for this species in the mean time, and those will not be a part of this file.