Found the issue couple of days before. So, thought of answering my own question, so that it will be useful for others.
The issue is Elastic beanstalk instance (Windows server 2019) already has VCpp redistributables installed and which is later version that I am trying to install as part of .ebextensions. So, when I tried to install, it failed.
I figured it out, by enabling RDP connection on the EC2 instance that is created as part of Elastic beanstalk and run the scripts manually, which gave a detailed error message.
Hope it helps someone in the future.
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