Hi,
Greetings from Best1
Yes we can entirely code the website in custom CMS and not WordPress like technologies.
The mentioned websites Amazon/ Flipkart/ Snapdeal are very big sites and have many features so do you want all of those ?
To arrive at an accurate time and cost estimation we need to discuss the project features in more details. So kindly initiate project communication so we can discuss in detail.
Regards,
Best1