Options to secure internal electronics
If you have a 3D printed box I suggest that you re-design the 3D data set to include printed in standoffs on the inside of the box that match the board mounting holes. These standoffs can be designed with a center hole in them so that you can mount your boards with short self taping screws.

Such standoffs would look similar to this one from a standard molded plastic enclosure. 



After all, 3D printing is all about customization - make use of it.