Yes -- the airlines are not like the hotel business in this regard (where you don't get elite benefits unless you book via their own dedicated channel). Mainly because most big corporate accounts go through AMEX anyway and the whole reason for elite status is to entice business travelers who have freedom to choose their own airline, to be repeat customers by provide them a non-monetary reward.

As long as you have DL flight numbers you'll have your usual benefits -- if you have AF/KL/KE or other codeshare partners but are flying on DL metal, you won't get C+ until day of departure (instead of clearing at booking) but you still get all the other benefits