I checked the code.
It seems to me that the issue is in this file:
https://github.com/yambo-code/yambo/blob/master/ypp/k-points/k_grid_printer.F
If coo_in=="alat" in input then this section of the file
do ik=1,nk
!
v=k(ik,:)
if (trim(coo_in)=="rlu") call c2a(v_in=v,mode="ka2i")
if (trim(coo_in)=="cc") call c2a(v_in=v,mode="kc2i")
!
does nothing.
I think a proper coding should be
do ik=1,nk
!
v=k(ik,:)
if (trim(coo_in)=="rlu") call c2a(v_in=v,mode="ka2i")
if (trim(coo_in)=="cc") call c2a(v_in=v,mode="kc2i")
if (trim(coo_in)=="alat") then
v=v/(alat_used_for_output/2./pi)
call c2a(v_in=v,mode="kc2i")
endif
!