I agree with what Gertie said, it can mean 'organised', meaning the arrangements have been organised with the organisation. Also, the example sentence is not strange, it is just out of context so it can sound odd.

Wow. What a weird sentence and horribly convoluted so as to be practically devoid of meaning. I don't know wrote this, but it clearly was not a native speaker. You'll have to explain to me what a "collocation" is because I've never heard this word in my life (and I'm a native speaker). Not saying it's not a word, but just a weird one and unusual. I haven't a clue what "in place" is supposed to mean in this sentence, which again is one of the worst I've ever seen. Like I said, it's so bad, I can only guess at the author's meaning. I'll try a little re-write to try to make sense of this mess. "An organization should be designed and operated in such a way that its facilities support a working environment for its people, and "systems." I'm not sure what "systems" has reference to, but I'll give the author the benefit of the doubt and assume it refers to computers, office equipment or something. All "in place" means is "in operation" but it has no place in this sentence, if I even am correct in understanding what the author meant.

In place = made, prepared, set. Everything is in place. = Everything is ready. Everything has been prepared. Everything is set. Everything is in order. Sorry I'm on my phone so I don't wanna type a whole lot. Hope it helps a bit.