There are transcripts (eg. AT1G08765) in Araport11_GFF3_genes_transposons.201606.gff which are not in Araport11_genes.201606.cdna.fasta. I did not expect this. Where can I find cdna.fasta which agrees with gff file?
The locus AT1G08765 corresponds to a novel transcribed region.
The Araport11_genes.201606.*.fasta files only represent the protein coding gene set. For novel transcribed regions such as this case, you can get the fasta sequence from the ThaleMine Gene Report page (URL below) and look for the "fasta" button under the Genomics section.