Revised return considered as original return

Hi

I have some queries regarding IT return for the AY 2016-2017 (FY 2015-2016).

My original IT return (u/s 139(1)) was e-filed within the due date (1 Aug 2016) by a CA on behalf of me. I was not residing in the country at that time. When I returned back, I realized that the ITR was wrongly filed. The gross salary figure was shown to be lower than actual which resulted in the ITR showing a large refund. When I did my calculations, I realized that I owed tax of INR 4090/-. I did not send the ITR-V for processing at CPC Bengaluru fearing that I would get a notice from IT dept. 

So I decided to e-file a revised return u/s 139(5) in order to rectify the mistake. I e-filed the revised return quoting the filing date and acknowledgement no of the original return, on 31 March 2017 (on the last day of the assessment year 2016-2017). Before filing the revised ITR, I paid the self-assessment tax of INR 4090/- using the TIN NSDL website. The payment of the self-assessment tax was registered on 31 March 2017 as per Form 26AS. The ITR did not calculate any interest u/s 234A on the outstanding tax amount of INR 4090/- I filed the ITR with nil tax balance. However, I e-verified the ITR on 1 April 2017. I did not send the ITR-V of the original ITR to the CPC Bengaluru as I thought it was not necessary as I have e-filed and e-verified revised ITR.

About 3 weeks later, I got an intimation u/s 143(1) from IT dept (section code 1431a). The outstanding demand is INR 320/- and the demand was uploaded by CPC (and they have rectification rights as well). When I checked the intimation PDF, it showed that the tax demand of INR 320/- is due to interest u/s 234A. Moreover, it showed me that the ITR is original instead of revised.

Questions:-

1. Why the ITR is considered as original? Is it because original ITR is now invalid as the ITR-V was not sent within the stipulated time period of 120 days? Also is the interest u/s 234A calculated because the return is now considered as original?

2. I agree with the interest figure (after doing my calculations). However, if I pay the outstanding tax demand and click on 'Agree to demand' using the 'Submit response' link in eFiling portal, will I be liable for any further action and penalties? As I am accepting that demand is correct due to late filing. I did manage to file ITR within the last day of AY 2016-2017 but everified it on 1 Apr 2017. Will that create an issue?

Awaiting your valuable opinions. Thanks!