I found the solution for this and it is an obvious solution too.
There is a node called "<profiledefinitions>" and a child node under that called " <profiledefinition>".
Using that you can easily put what ever the profile attributes that you need to put when installing the site.

Here is a sample section from the .template file

<profiledefinitions>
<profiledefinition>
      <length>50</length>
      <propertycategory>MyCategory</propertycategory>
      <propertyname>NewProfileAttribute</propertyname>
      <datatype>Text</datatype>
    </profiledefinition>
...
</profiledefinitions>

Further you can review this by exporting the portal template by login as host.
Host>Portals>Export Portal Template