Translation:When was the train supposed to be here that we are waiting for?
Question to the natives of English: doesn't that English sentence sound weird to you? I would insert this that-clause in the middle.
The word order that you suggested is an accepted translation. The English natives on the course team feel that, while your translation is more natural, "When was the train supposed to be here that we are waiting for?" better reflects the Czech original.
What about the word order "When was supposed to be here the train, that we are waiting for?"? Is it correct in English? Thanks.
I have no idea what you are saying. Perhaps you can illustrate it using some example?
There are (currently) 66 accepted alternatives, but only one can be the "main" translation. Usually -- but not always -- that's the one that sounds most natural in English. In this case, the translation shown seems like a better tool for teaching the Czech sentence structure, although it is not ideal in English. However, it's possible that this may be reconsidered in the future.