Yes, it is about charging of interest for default in payment of advance tax, as the statues says, but how the ITD is using this section is in a bizarre way.
The Provisions of section 143(3) are applied is such a way that despite refund of tax after disallowance(s) if any, no refund is granted in the assessment order.
And to set off that refund due to the assessee the entire amount of admissible refund is adjusted under the head of section 234B, whereas , in those cases 234B whether applicable or not.
Is it justice and compliance of the law. NO officer is willing to grant you refund in 143(3) assessment order, for the fear of decline in revenue and recovery amount under its charge. Although the statues permits to grant refund but the statutory provisions are flouted in concerted manner by the entire department
The relevant part of section 143(3) says:-
4[(3) On the day specified in the notice,—
(i) issued under clause (i) of sub-section (2), or as soon afterwards as may be, after hearing such evidence and after taking into account such particulars as the assessee may produce, the Assessing Officer shall, by an order in writing, allow or reject the claim or claims specified in such notice and make an assessment determining the total income or loss accordingly, and determine the sum payable by the assessee on the basis of such assessment;
(ii) issued under clause (ii) of sub-section (2), or as soon afterwards as may be, after hearing such evidence as the assessee may produce and such other evidence as the Assessing Officer may require on specified points, and after taking into account all relevant material which he has gathered, the Assessing Officer shall, by an order in writing, make an assessment of the total income or loss of the assessee, and determine the sum payable by him or refund of any amount due to him on the basis of such assessment:]
NOW the remedy is you take it as mistake (albeit deliberate mistake) apparent on record and get it rectified and amount refunded, of course, it is matter of prudence, visitingthe doctor twice, fee required to be paid again in commensurate with the quantum.