csv file operation: compare two csv files and return all matched line with header
You may use another condition FNR == 1:
awk -F, 'NR==FNR {A[$2,$3]=$0; next} FNR == 1 || ($4,$5) in A' f2 f1
ID,type,gene,startpos,endpos,product
C20775336,marker,gene1,1895,2166,ID=gene1;Name=maker-C20
C20775337,marker,gene2,895,1166,ID=mRNA1;Parent=gene1;N
C20775335,marker,gene4,2795,2962,ID=CDS1;Parent=mRNA1
C20775338,marker,gene5,895,1166,ID=mRNA1;Parent=gene1;N