Actually, you can change the priority order fairly easily.
1. Go to the %APPDATA%\Microsoft\QuickStyles folder (or wherever you saved your QuickStyle template). Find the .dotx file that you want to change.
2. Using WinRAR or any archiving utility that recognizes zip files, open the dotx file and extract the contents (somewhere).
3. Within that extracted archive should be an XML file called styles.xml under the "word" directory. Upload that to an XML formatter of your choice. I just googled "Free Online XML Formatter" and found one. That will make it easier to read. Save the file from the XML formatter back to where you uploaded it from (or copy the output to your clipboard to paste into the styles.xml, replacing all the stuff that was already there).
4. Open it in notepad or any text editor, and look for a section that starts with "<w:latentStyles". Within that section you should see all the styles for that template. They'll look something like this:
<w:lsdException w:name="heading 1" w:semiHidden="0" w:uiPriority="9" w:unhideWhenUsed="0" w:qFormat="1" />
5. The priority numbers are shown in the "w:uiPriority" values. Change them to any order you want, or set them all to 0 if you want the styles to be sorted alphabetically.
6. If you want to backup your old dotx template, do that now.
7. Now make a new zip archive containing the same files and their directory structure and save it to your %APPDATA%\Microsoft\QuickStyles folder, making sure to change the extension from zip to dotx.
Done.