In the context of the cited language, the word "order" is not being used in the context of a military style command, instead it is being used in the context of a purchase order for goods or services (or a contract) that has already been voluntarily entered into by the parties. The overall context is a statute about military procurement of goods and services, not about deputizing civilians to act as involuntary federal investigators. This is about how already existing defense contracts are to be performed by defense contractors, not about anything more profound than that.
It is saying, for example, that if the Air Force purchases 100 iPhones from Apple that the President can insist that it fulfill the Air Force's order of 100 iPhones before it fulfills any other customer's orders (even if they pay a rush fee or are related to the CEO or something).
The cited language does not confer upon the President a general authority to make anyone do whatever he tells them to do for national security purposes. As such, this statute does not authorize the President to tell Apple to decrypt a phone even though there may be some other statute, completely unrelated to this one, that does authorize the President to do that under some very different circumstances. I won't venture to have comprehensive knowledge of all U.S. laws on national security, but the one quoted doesn't get the job done.