Transporting the theme created with the UI Theme Designer is possible. I think this is a workaround, so bear in mind this can change. The workaround is necessary since transporting it via a normal way does not work yet.
What happens when you edit a theme?
When you use the UI Theme Designer, all changes are stored in the Web Resource Repository. A new folder has been created called theming. Here are all the LESS files stored, but also the generated css files. Do NOT edit the css files. But you can edit the less files (see my previous post).
Besides the LESS and css files, you will also see the theme appear in the PCD themes folder.
Step by step workaround
Step 1: Create a portal transport package
Go to System Administration > Transport > Export and navigate to your transport folder. Right click and create a new tranport package. Now you can add the theme.
Step 2: Add your custom theme to the package
Select in the PCD the theme folder and then your custom theme. Right click on it and add it to the transport package.
Step 3: Add WRR folder theming
Now add the WRR folder theming to the transport package. If you have multiple themes, you will have to expand the folders below till you see your custom theme to transport. Since I have only one custom theme, I selected the whole theming folder.
Step 4: Finish the portal transport
Now you can transport the theme package to the acceptance server. But..... There is no trigger to rebuild the theme on the acceptance server. You will need to do this manually.
Step 5: Rebuild theme on acceptance
Open the acceptance server, go to Content Administration and select Portal Display. Open the UI Theme Designer and select your theme. Edit it.
Now the theme is being loaded. You will see the Test suites in the preview pane, UR Control Previews and Portal Control Previews. The thing you need to do is to Publish your theme again, but that option is not available at first. Select UR controls and check one of the UR controls (doesn't matter which one).
Now in the preview pane the UR control is being displayed. The Quick and Expert tab will display information. You don't need to change anything however.
Step 6: Publish theme
Now the Publish option is available in the Theme menu. Publish the theme and you might get a warning that it will take long. Just wait...
When it is done publishing your theme should be available at acceptance!
Step 5 and 6 can also be done with a portal application. I never tried it (since I was told by Itzik and Shani to use the UI Theme Designer :-), but the application is:
http://[servername]:port/irj/servlet/prt/portal/prtroot/com.sap.portal.themes.archive.download
In this case replace the servername with your acceptance server.
Hope this helps you 
Index:
How to... UI Theme Designer - Installation
How to... UI Theme Designer - Locating elements
How to... UI Theme Designer - Transportation (you are here)
Happy branding,
Noël Hendrikx
Peppie Portals