From the sounds of things, the encounter was fine.
In that I was asked to allow a search of my vehicle for no real reason.
This seems to be a real hang-up for you, so let me see if I can explain it. Obviously I wasn’t present for any of this, so take what I’m saying with the appropriate grain of salt. First, the Border Patrol catches thousands of smuggling cases each year. That’s not a figurative statement; it’s a literal one. That particular PA might very well have been involved with hundreds of smuggling cases in the course of his career. Doing anything that many times is going to give somebody a few seeming inconsequential bits of knowledge regarding smuggling tactics. He wouldn’t tell you, but its entirely possible that the particular type of vehicle you drive is a common type they see smuggling aliens. Additionally, your actions might have created some suspicion. Probably nothing huge, but little things like maybe the speed you were driving or something similar. Also, you wouldn’t be made aware of this, but it’s entirely possible that they had something that led them to believe somebody was about to pickup a load of aliens. Maybe they had busted up a group in that area. Or maybe they had gotten a citizen report of a group. Or maybe they had chased a group back across the border right before you arrived and they suspected that the group would try to cross again and this time load up in a vehicle instead of trekking across the desert.
My point here is that it is more than possible that there was a lot more going on than the PA told you.
Edited to add:
The fact that he asked to search doesn’t mean he didn’t have any suspicion. He was just looking to satisfy himself that everything was “kosher”. Something (or several somethings) looked a little out of the ordinary to him. Remember, he’s probably been involved with many, many smuggling cases, and he spends
way more time in that specific area than you do. He tends to notice when things are done out of the ordinary, which is often indicative of something going on. You wouldn’t let him search, he looked through the window and probably accomplished the same thing. Had you given consent when he asked you wouldn’t have give up your right to privacy, or unreasonable search and seizure at all,
he was asking permission. I suppose it made you feel better, and it’s certainly your prerogative. What you really accomplished though was to make him think that shooters around there don’t like the Border Patrol and don’t really appreciate what they do.