1. there is no difference between publishin a site and just copying it except for: files are not compiled and are slower at first run.
2. notice dlls that are in GAC are not published with the site
3. Machine.Config is never published with the site, so behavior of the site may differ
there is 3 options:
1. The Allow this precompiled site to be updatable option
specifies that all program code is compiled into assemblies, but that .aspx files (including single-file ASP.NET Web pages) are copied as-is to the target folder.