These crates by rodrigorosseto are some of the best battery storage options I've seen on Thingiverse thus far.

https://www.thingiverse.com/thing:4906830

I took his designs as well as the empty crate made by Corish (https://www.thingiverse.com/thing:4915186) and made some small modifications so that I could print them stackable and without supports.

If your printer has decent cooling, it should be able to bridge the archways as well as the stacking-groove.

The only real difference is the stacking mechanism. Instead of using rodrigorosseto's stackable rim, I extended an inner ridge on the top of the crates and created a matching groove on the underside. The result is that the bottom lays flat against the bed when printing, and there are no supports to remove afterwards. I'm not a fan of supports when I can avoid them.

Update: I've added the genius re-design for CR123s by coldfire0200 (https://www.thingiverse.com/thing:4921755) which uses hexagon spaces to fit more cells in the crate.

I've also added a couple of lids that will line up with the stacking-ridge and clip in place. There is one thing to take note of though:

The lid works with 5 out of the 7 crates. However, because of the way the batteries line up inside the crate, the lid with 2 clips will not work on the crate for AA batteries or the AA/AAA mixed crate. For those two crates, you need to use the lid with the four (4) clips. I've printed them without supports and although there is a little distortion at the first edge of the clips, they still work just fine.