I would think that the 200 IFR hours have to be in the operation for which we would teach it.
Meaning: Single Pilot.
That might be a logical conclusion if logic or relevance had anything to do with it. What you need to realise is that European legislation is all about keeping low quality lawyers in permanent employment. Much of the aviation legislation is a straight copy from the FAA, but with European tinkering at the committee level thereafter, it is left to administrators to process it and they probably wouldn't know the front from the back of an aeroplane.
if I work at an airline, flying the big jet (so multi pilot under IFR), would it counts towards the 200 hours required
Indeed it will and this is probably the only way many instructors will acheive it.