>>No. I was assuming that you publish the development web.config (or at least a web.release.config) when deploying. Changing the target framework on the deployed app could be risky if you've compiled your dlls for a different version....
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>I never use those features. I have my own command center and when I deploy, I click on the DLL for the Web site, select the server and that's it.

My point was that, regardless of how you deploy, the web.config produced by VS is heavily dependent on the Target Framework selected for it's project. As an example try 'downgrading' a .NET 4.0 web project to .NET 3.5. and compare web.config before and after. Modifying the .net target settings directly in the web.config on a production server where DLLs have been compiled using a different version seems inherently risky.....