Sharepoint : Customizing ONET.XML of MySite (SPSMSITE) template
Customizing ONET.XML of MySite (SPSMSITE) template
In the template folder you will also find the default template for the MySite configuration. You might think this works in the same matter as the other templates, but no. Editing the default.aspx in the SPSMSITE folder has the same effect, but altering ONET.XML has no effect. This is due to the fact that Sharepoint creates the virtual site that handles all MySite sites on installation, thus only processing the ONET.XML in the SPSMSITE folder once. To alter the MySite template for all users on your portal use FrontPage and navigate to your RootSite/MySite, then perform your changes.
This inconsistency is kind of hard to spot, and reduces the possibility of preconfiguring the setup of a site before it is rolled out. Not much to do about that though.
Ref : http://weblogs.asp.net/mnissen/articles/68629.aspx