Which identifier do I have to use when I want to add a ##Fasta section to a gff?
Unless I'm mistaken, the only variant of GFF that explicitly permits Fasta entries is GFF3, and the data you've shown above is definitely not valid GFF3. The mRNA entry seems to correctly use the = symbol to separate keys from values in each attribute, but the remaining columns all use spaces and quotation marks (GTF style) instead. This is likely to cause all kinds of problems with software packages that take GFF data as input.

But to more directly address your question, there is no "right" way to connect feature entries to sequence entries in a GFF3 file. There are some conventions, but these are all very specific to a small set of tools and community of practice, and it is rare that these conventions are objectively enforced. Some options include:


Placing genomic nucleotide sequences in the ##FASTA section, and then using feature coordinates to pull out mature mRNA sequences and translate them in silico to derive the corresponding peptide sequence. In this case, the Fasta entries would be genomic sequence identifiers that correspond to the first field/column in each feature entry.
Placing mature mRNA sequences in the ##FASTA section, and then directly translating this sequence to derive the corresponding peptide sequence. In this case, you'll want the sequence IDs in the ##FASTA section to match the ID attribute of the corresponding mRNA feature.
Placing the peptide sequences directly in the ##FASTA section. In this case, you would either want to have protein features declared in the GFF3 file (uncommon) or have some sort of protein_id attribute associated with each mRNA feature, in which case you'd want the sequence IDs in the ##FASTA section to match this protein_id attribute.


There are probably other ways of doing it, too. Which way is "right"? The GFF3 specification has nothing to say about it. It depends on the tools you are using to do the subsequent processing and analysis. If you're lucky, those tools might even document what they expect in terms of input.



Let me just say, as a post-script, that I think placing sequences and feature annotations in the same file is a horrible idea. I've never liked this about GFF3.