There are a few different ways to emphasize crepuscular rays in post production.

1) One of the ways those crepuscular rays can be enhanced is with any tool that can provide volumetric lighting effects. The one I use is a tool called Rays from Digital Film Tools. As you mentioned, this type of tool may be the type to add fake rays to a photo. However, I don't like using it for that, I just use it to enhance only what's already there. That is, I recommend a 'less is more' approach.

2) Another way, using Photoshop, is to add a shaped/mask, gradient layer above the photo layer and set the layer to screen. You'll have to shape the mask to just the light beams by hand. Then feather the edges of the shape, and either blur the shapes or use a gradient layer.

3) Another Photoshop option is to apply selective contrast / micro-contrast to different parts of the image. Like in the prior technique, you'd apply changes to a masked area.

4) If you have Lightroom you can use it's masking capabilities to selectively darken parts and lighten other parts of the image.

I'm sure there are other ways, but those are four post-production techniques I can think of at the moment.