Hello hometime and
There is a Patch
at the Neebla Games
I don't think that it corrects what you need.
With or without the WT, you can finish the underground area and touching the core will bring you back to where the game started. At least that's what it does when doing the underground last. When you have all the Cores, you go back to the dome where the girl is to finish the game.
I remember at one point that the writer (Bert Jamin) of the WT did rewrite it to use the sequence given by the present WT.
Now, when you come back from the underground and do the other areas (if you can), will it permit you to finish the game, I do not know.
You could contact Bert with his e-mail address on top of his WT.