You could make a Simplified Annotation Format (SAF) file from your GFF3 and use it with featureCounts. Much easier to do than modify source code. Here is an example from featureCounts manual.

GeneID      Chr Start   End Strand
497097      chr1    3204563 3207049 -
497097      chr1    3411783 3411982 -
497097      chr1    3660633 3661579 -
100503874   chr1    3637390 3640590 -
100503874   chr1    3648928 3648985 -
100038431   chr1    3670236 3671869 -

Don't modify complex source codes, this will only run you into trouble as you are not aware of the internals of the code. Make it simple, either by creating SAF as genomax recommends or by transforming the gff3 to gtf Convertion Of Gff3 To Gtf