One thing hinted at in the article is the risk of harm to "innocent" drivers from drivers carrying drugs who are distracted by the large scary yellow signs, and thus driving while distracted.
> Peters said the officer asked him what kind of drugs he had in the car, saying it would be much easier to confess before other officers and a drug-sniffing dog arrived. Peters insisted he had no drugs. As promised, other officers and the dog were summoned, and Peters agreed to allow his car to be searched.
I'm not a lawyer, but as I understand it you shouldn't agree to be searched. What's the current best practice for this?
 using the words of law enforcement to emphasise the point.
There is literally nothing good that can come from giving up your rights if you are innocent (for you personally, for the police, for society).
No, the police would like for you to think that. But imagine this scenario. You just dropped off a few friends. One may have dropped his prescription pain killer in between the seat cushions. Now, you've consented to the search and they found that dropped pill. You have no recourse, no prescription for a controlled substance and all you can say is it's not mine and you don't know how it got there.
Know Your Rights - Don't Talk to Cops Part 1
That said, it is possible that a trained canine might have alerted from
outside the car, generating enough probable cause for a legal search
inside of the car without consent of the driver.
This is an area that has seen a lot of litigation in the last 30 years or
so, for details google "probable cause" "canine" "Place" "Jardines"
"Harris" and "Caballes".
Only difference is they didn't search 100% of the cars.
If a driver appears to be drunk, how is that a random stop? Isn't that a 'probable cause' thing?
They're not stopping drivers who "appear to be drunk" - that's the point. They are allowed (supposedly, IANAL) to set up a checkpoint to stop every car (effectively a random stop) that passes by to see if the driver is intoxicated, or check to see that they are not in the country illegally.
They're not allowed to check for other crimes without probable cause though. They can't set up a check point to say drug possession or tax evasion, though if you are at a DUI checkpoint I believe you may somehow give them probable cause to check for those things.