Sill plates (thresholds) before floor tiles or otherwise?
In terms of the general process it's acceptable to do it threshold(sill plate) first but there may be specifics to the situation that we're not aware of. Contractors are primarily concerned with pushing the project along to keep pace, but occasionally to do that you have to do things out of sequence. An example would be, if the threshold is available but the tile isn't in yet, a contractor would be tempted to set the thresholds first. This might make it look like progress is being made but it could ultimately make your tile guys job a lot more difficult. If the guy contracted to do the tile work wants to do it a particular way, I would trust his/her judgement unless the contractor can produce a very compelling reason not to. In the end (however they do it) if the finished product isn't satisfactory it's on them to make it right.