It's been theorized that the real Leonardo da Vinci was gay or asexual. That Leo Took a Level in Jerkass from the moment Thena joins them can be explained by his discomfort at having to deal with a woman for more than a few minutes.
Except Leonardo spends a considerable amount of time hitting on her in the movie. He was annoyed by Thena tagging along and getting involved in Delta Knight stuff when she wasn't a member of the Order. Then they seem to fall into a Belligerent Sexual Tension thing that fizzled out from the story because this movie sucks. And Leo is a jerkass anyway.
In one scene, Baydool asks Tee his name in English, then in French, Spanish, and German... but he seems to wait several hours in between each time. The first time he asks it's early daylight and the last time it's dark out. Why would he do that?
How do we know he didn't spend all day trying out different languages?
After Tee decides The World Is Not Ready for Archimedes' secrets, they ride off, presumably leaving the location of the library lost. So what exactly would stop Thena from coming back with a bunch of her brother's men and digging the library out? It's not like Tee made her promise to leave it or anything.
Thena did say Tee was right, so she probably felt it was best to leave it.
Everything was destroyed by Vultare overloading the first thing he touched anyway, Tee's bombs just kept the blast contained.