No, it’s not the same logic because there’s two different numbers: border crossings versus deportations. Nobody is saying the numbers are “cooked.” Just that you have to understand the methodology to compare Obama and Trump.
The LA Times article explains that the deportations number includes deportations of people who were caught shortly after illegal crossing. During Obama, there were a large number of border crossings. So anyone who got caught shortly after crossing was counted as a deportation. But border crossings dropped to nearly zero under Trump. That drives down the deportation numbers. The low hanging fruit is gone.