A. This isn't actually a virtualized application vs. local application problem. It's just a general consideration whenever you have multiple applications that have the same file type associations. Essentially, whichever application was installed or published last will own the file type association.
If you have Office 2010 installed locally, the local Word 2010 will be associated with .doc. If you then publish a virtualized Word 2003 to the same machine that has file type associations for .doc files enabled, the App-V Word will be the default application for .doc files. You can manually change the file type association or you can remove the file type association from the virtualized application so the locally installed Word would still own the file type association.
You can change file type associations using the Default Programs, Set Associations Control Panel applet, as shown here.
You need to be very careful when deploying multiple applications with the same file type associations to avoid random behavior based on installation order. You should always make a spreadsheet of applications and their file type associations and make a decision on which application should own the file type association.