Many companies easily drop a $10,000+ premium for a prototyping kit every day of the week to get support from a preferred vendor. If you give one employee making 150k/yr a 10% productivity boost, you're saving money. Prototyping cost is often mostly labor. Unit cost doesn't really matter as much until you're talking about the production BOM.
Some rough math, for an employee with a 200k fully loaded cost working 1800/hr/yr, the difference in the price of those boards is about 8-9 minutes of labor. So if it's 10 minutes quicker to get the documentation for the Arduino -- it's cheaper.