Hi Sunny.
Nice having you in Microsoft community.
I just tried to find ways I can set copy and paste in my OneNote 2016 advanced setting configurations and unfortunately, I could not find this option there. However, there is a quick and efficient method to paste into OneNote 2016. Just right-click on the location where you want to paste your content and press T. It will only paste with Text.
I have seen this to be convenient and time saving.
Anyway, the best solution to this problem is to alert the product and engineering team to be aware of the problem by sending feedback. In your OneNote 2016, go to File > Feedback. The feedback you provide goes directly to the product and engineering team.
Regards,
Christophe