tl;dr; Clicking OK is the workaround, everything will work fine after that.
I also received this error message.
Configuring Web http://localhost:xxxxx/ for ASP.NET 4.5 failed. You must manually configure this site for
ASP.NET 4.5 in order for the site to run correctly. ASP.NET 4.0 has not been registered on the Web server.
You need to manually configure your Web server for ASP.NET 4.0 in order for your site to run correctly.
Environment: Windows 10, IIS8, VS 2012 Web.
After finding this page, along with several seemingly invasive solutions, I read through the hotfix option at https://support.microsoft.com/en-us/help/3002339/unexpected-dialog-box-appears-when-you-open-projects-in-visual-studio as suggested here.
Please avoid doing anything too drastic, and note the section of that page marked "Workaround" as shown below:
Workaround
To work around this issue, click OK when the dialog box appears after you either create a new project or open an existing Web Site Project or Windows Azure project. After you do this, the project works as expected.
In other words, click OK on the dialog box one time, and the message is gone forever. The project will work just fine.