Thanks for getting in touch, It's great to hear you are considering plugin development.
Geneious does have importers and exporters for both BAM and GFF3 which you can call programmatically from your plugin. The main challenge I can see for you will be around importing the results.
Firstly you cannot export GFF on an alignment, you will have to call it on the reference sequence stand alone.
Secondly, I would recommend including the reference sequence inside the GFF file or as a FASTA file that is imported into Geneious at the same time as the new GFF expression data. Attaching calculated expression levels to the original data is not really possible via the API right now without a fair amount of work.