Thanks to ocratato over at fedoraforum who had the simple solution of omitting the %u or %U and including a "-new-tab -url" for the first url (I hadn't included it before the second url) as well as any other urls. It just won't work with out it being present.
Example:
[Desktop Entry]
Version=1.0...
Hello,
Noob Alert. Just joined hoping someone can help with creating a Desktop Entry to launch a new Firefox instance with multiple tabs. The -new-window part is easy but I can't find anything about multiple tabs.
If I do something like "Exec=firefox %U -new-window url1 url2"
The new window...