I prefer Pred's method of sliding magnets horizontally into pockets to just having vertical holes in the base of my bins. I couldn't find an existing model for that, so I modified Pred's bin F3D to have just the base profile and a plate.
Configuration is done through Modify > Change Parameters. Width_X and Width_Y control the number of rows and columns the profile has. BottomThickness controls the depth of the plate on top of them.
In addition to the source file, I've included a few sizes that I use regularly. Comment if you'd like different sizes and can't figure out how to generate them!
Insertion jig: https://www.printables.com/model/637308-magnet-insertion-jig-for-preds-parametric-gridfini
The author remixed this model.
Removed the upper part of the bin, leaving just the base profile.