I have gone through many of the articles in online, and doesnt seems the problem is because of that.
When I browse one of the getresource url (https://domain name/CMSPages/GetResource.ashx?stylesheetfile=/App_Themes/Default/bootstrap.css), it will take me to front facing site with pagenotfound error instead of downloading the css, which is fine because thats the problem. But here on front facing site the getresources seems to work (attached image)
Which means, getresource does not work for backend cms only. I though its because of ssl, but I use https. Also the folder permissions are all good.
I could not understand why it gives me 404 for all the assets on cms site and works fine in frontend site.