Well perhaps it is part of the "secret" and mystery. I know there are many connections between runes and the world tree. But nowhere on the album is the connection really stated. Maybe I haven't studied the lyrics enough. It just seems to talk about the world tree to me.
About the other question, I think of Thomas as a band member. Sometimes I think that Therions lyrics are not genuine, they are not what the authors of the music feel or think. They write the music then lyrics are given. But the lyrics seems to go with the songs so well, it really works. Take Kali Yuga, the riffs at the start and the whole sound reminds me of chaos, destruction. Ljualfsheim I feel as though I'm being carried away by beutiful light elves just by the sound of the music itself. Maybe not on all the songs, but most of them the sound fits the lyrics. Thomas has a real gift for listening and hearing what the songs are saying. They work so closely together that it is like he is part of the band.
Its a different thing when you take, say Kelly Clarkson. Some team of people make a beat. Some other guy writes some lyrics. She goes in and sings random lyrics over top of a random beat. That's not authentic to me. What therion does is.
The only thing that may not be authentic is the singers. Singers should really feel the emotion of the music, moved by it. That's why usually the singer is the writer of the lyrics. They need to feel what the song is saying and convey that. This is the weakness of having many singers is that you can't do this so well. But there are so many more strengths that also come with having so many singers so it is a worthwhile trade. And it is more like classical where different performers perform the same piece. Yet these songs are new, unlike hundreds of year old classical pieces so it is harder for the performers to interpret and feel the songs as deeply as some classical performances. This is probably why Tarja is popular from Nightwish. Her opera singing is not as good as some others, but she puts the proper feeling into it with context to the music.
Despite this, a lot of the lyrics have a lot of feeling. Lemuria for one. Perenial Sophia. Others probably would be better if the singers became one with the lyrics, understood them more, felt them more. There seems to be a lot of little places where it shows itself as a weakness though (especially with singers that aren't native speakers of the languages they sing). In wisdom and the cage, it seems like he says "I am locked when heavy chains" instead of "locked with heavy chains" there were some lyrical mistakes in Aldruna that were mentioned in TS that Chris clarified. I think there were some mistakes in Siren of the Woods too. Some of it is unavoidable when dealing with so many different languages and is not a big deal, but the emotion of the song could probably also be stronger in some cases. Though I think generally the singers of Therion enjoy the music, they feel the mood of the instruments and do a pretty good job putting the right emotion into it, even if at times they may not understand the lyrics completley.
Also what makes Therion different is there isn't a lot of emotion in the music. Which I think is good in that its different but sometimes can leave you wanting more. The lyrics aren't about love, romance, beauty, sin, pain, heartbreak, sorrow. They are mostly about spiritual and occult things from a mostly intelectual very masculine perspective. Some songs have connection, perenial sophia, Call of Dagon etc. have some emotion. but compared to Nightwish, Leaves Eyes, or other bands of that nature, not a lot. So I suppose this type of lyric is more suited for singers who aren't as familiar with the emotion and meaning behind it.