I'd be surprised if they could detect battery swelling on a scanner. The battery's horizontal area doesn't really change, it just kind of bulges. The scanners are two dimensional and they make you lay your computer flat in a separate bin so it's not like they could detect vertical swelling.

I also had a similar reaction to my 2014 rMBP once (and only once, over a few dozen flights). I figured MBPs just look scary from the wrong angle, or maybe new scanner employees who haven't figured out what all the common laptops look like yet.