I have been hacking around a bit in the S60 3rd ed FP1 SDK, and I think I found out why it was a bit hard to add extra screensizes, in particular for E90 screen emulation.
It turns out that S60 uses more than one wsini.ini's. There's one in in epoc32\data and there's another one in epoc32\release\winscw\udeb\z\system\data. It isn't yet clear to me which one is actually being used by the S60 3rd ed emulator, but if you look at the UIQ 3.0 emulator, there is no wsini.ini in in epoc32\data, while there is one in epoc32\release\winscw\udeb\z\system\data.
Back to getting multiple screensizes on the S60 3rd ed FP1 emulator. What I knew was that the S60 3rd ed MR SDK has multiple screensizes so I decided to copy the files related to the screensizes (the wsini.ini files, wsini.icl form epoc32\release\winscw\udeb\syste,\data and the epoc*.ini files and their associated bmp's to theS60 3rd ed FP1 SDK). Make a backup of the target files first if you don't want to reinstall the FP1 sdk.
Starting the FP1 sdk, and lo and behold, it now has the same screensizes as the MR sdk. You can see it's the FP1 sdk because of the startup screen. FP1 has the twirly colorfull S60 logo, and starts in the standby screen, while MR just goes straight to the Menu screen.
Anybody has a good highres shot of the E90 for making an emulator skin?