FP2003 already supported Master Pages. They're called DWT, or Dynamic Web Templates. The question is will you have to use only FP to modify Master Pages, since this is a native component of the vs.net 2005 ide. Personally, I think forcing developers to use FP to edit/customize Master Pages is going to cause MS and SharePoint a lot of grief. The basic functionality is already built into vs.net 2005, but you'll notice that you can't open a WSS / SPS site with vs.net 2005. Blah. <inserts flapping gums here>. Nothing really positive to say about that, so will just say I am not in favor of it.

@Christopher:

DWT and Masterpages are not the same. DWT is designed especially for use within Sharepoint and the masterpages we are referring to here are from ASP.NET 2.0.

In fact, the new Sharepoint templates will derive from ASP.NET masterpages.
For as far as I know it won't be necessary to use FP persé if you want to edit a masterpage. You can just alter the file on your harddisk and change the look of your entire (already created) portal at the same time. So no more hassle with implementing the same logo-bar on a lot of templates.