I faced every possible problem that could have happened, sadly. I ended up paying 27.73% duty, Rs 500 as bonded warehouse charges for the delay , Rs 27 interest on that. Rest everything is legitimate. 2.5 % of duty amount as DHL's fee for paying upfront duty on my behalf + GST on that and Rs 2600 as clearing charges that is all.
In the end getting IEC was the only thing that worked for me, even though that is clearly not required for people like us. But I'll cover all these things in a dedicated thread on what to do what not to do and what all is required.