“How much time does that leave for actual training?”
An excellent question.
A 100% lockdown (everybody confined to a holding area) until everyone has given a sample will easily kill half a training day. If applied correctly, the program is supposed to test ten percent of personnel each month. The first sergeant calls out names randomly selected by SSN, and everyone else goes about their business. This keeps the actual druggies on tenterhooks as it was designed to do; for the rest of us it the same invasive, degrading, guilty-until-proven-innocent procedure it has always been since introduced in 1972, our last full year in Vietnam.
Now, somebody said that “alcohol is at least as dangerous as marijuana”. That is nothing but an opinion unless backed by volumes of facts and statistics, so the assertion is a non-starter.
My whole argument is that compulsory urinalysis, like airport security searches, are the result of the misdeeds of a few, for which the majority (and liberty itself) pays a considerable price.
Your analogy to airport security screenings is a poor one. At the airport, we are attempting to keep those determined to commit murder from getting on airplanes. They are bent upon doing something that the vast majority of people consider evil and immoral. Acts such as murder are immoral in and of themselves and require no laws to define them as such. Drug use, on the other hand, is not so universally condemned. Some drug use, such as alcohol consumption, is even socially acceptable. Drug use is not an act that is immoral in and of itself. It is only "evil" because the law says so. Take away the law, and the definition as "evil" goes away too. Not so with murder. Murder is evil with or without a law saying so. (In legalese, this is the difference between Malum in se and Malum prohibitum.)
Thus in your case, you are not being told to pee in a jar because a few bad apples are intent upon doing some horrible evil, but because some politicians didn't like their choice of a recreational intoxicant. (Do you suppose said politicians toasted the passage of their drug laws with a few adult beverages?)