Learn English – Use of “Align with”

Prepositions like on, with, and in are indicative of the writer's intent. In your example sentences

I work on a team.

the preposition on means that the subject works as a member of a team.

I work with a team.

the preposition with means that the subject works in a cooperative way, although it could also indicate membership of a team.

I work in a team.

the preposition in in this case seems to mean location within a team, but this does not convey the same sense of participation suggested in the first two examples.

As to whether this is a matter of word choice or collocation, it is word choice to convey intent. Collocation most usually refers to several words that are often used together (e.g., making my bed, bar of soap, burst into tears). Collocation for your examples might be something like work team or perhaps work in tandem.

"It's XY through whom ..." or "it's through XY that we have ..."

The sentence is correct grammatically. You can also say:

We have established non-standard relations with our partners through XY.

However, the first sentence, which is a cleft sentence with the use of it's, emphasizes the subject XY, and the second sentence is a simple sentence.