I've integrated winstep into my unnattended install of windows but was wondering
if there is a way to get ATMOSPHERICA

To be the default theme rather than the Aero low Rez?

Nope, sorry, because Aero as the initial theme is hard coded into the software - Atmospherica is also not available in the theme pack that ships with Winstep Xtreme by default.

That's okay, i figured it out:
I made it into a portable and then launch the portable with all theme settings intact.

What do you mean - portable? As far as I know winstep is not portable-aware application (at least Workshelf). I did some tests and I discover that it is impossible to change Workshelf config to works with relative paths.
If settings are backed-up to a *.wbk file and then all paths like "D:\Common Applications\Winstep\Themes\Brisa" are changed to "Themes\Brisa" and this file is loaded by Restore function on General Preferences page and then again backed-up then some relative paths are invalid resolved.
After restarting Windows Workshelf have completely different theme than set earlier (i.e. tiles instead theme).

Besides, how you can make portable version when all settings are stored in registry? Do you mean that you carry Winstep on USB stick and merge winstep REG file with settings to every computer on which you launch it? This is not portablility.

Or maybe you made winstep portable version by application like Thinstall?

I'm very curious.

BTW It is strange that if you backup/restore settings few times with exiting preferences dialog box and quiting WS in between, but without change ANY setting then saved *.wbk files have many differences between themselves.

Without an ASCII comparison between two .wbk files, there isn't much I can tell you about those results. WorkShelf does save information that changes from time to time into .wbk files - such as the time the Atomic Clock and Weather Servers were last checked, etc...