Going Through the link I feel its possible to apply a general rate structure and when there is exceptional rate like a cess mention that in that particular item which supersedes the general rate structure for the HSN code.
Also there is no reasoning that one wants to use 2 digit or 4 digit HSN code as duties like custom duty are always levied on 8 digit code.
If you want to still use only 4 digit you can always set length of code to print like left(code,4) in excel.
But this brings me to a point how can same HSN code have different GST rates unless you are using improper classification or 2 or 4 digit HSN
Also Please stop comparing with other software we are here to make erpNext better than the once exists and call themselves market leader ! The sad part is I am forced to use one and its quiet a Pain and I am turning in to an accountant from engineer