When you’re doing a long involved investigation and your suspect makes a run for it, you bust him on the charge you currently have pinned down. That keeps him around until you can complete the other investigation and it keeps him from getting a heads up on what else you have. It’s basic cop-craft.
I think you are exactly right. With no passport and under GPS surveillance he’s not going anywhere now. And his chances of survival are probably better on the outside than if he was in a controlled environment like a jail where “accidents” can happen any time.