I know that you are free to do it because IBM promises backward compatibility, however, here's what's in Domino 6's help:
"Virtual Server document
The Virtual Server document applies to releases of Domino prior to Lotus Domino 6 only. The Virtual Server document establishes a new Web site on a multiple-site server, that is, a server that is configured to host multiple Web sites. The settings in this document override the corresponding settings in the Server document."
I recommend that you consider using Web Site documents.
Here's a small reference for moving from old to modern configuration:
http://www-01.ibm.com/support/knowledgecenter/SSKTMJ_8.0.1/com.ibm.help.domino.admin.doc/DOC/H_R5_WEB_SITE_TO_RNEXT_OVER.html?cp=SSKTMJ_8.0.1%2F1-11-0-1-0