Problem using Texture Packer with alpha channel

I'm working on a game that has a lot of plants in a scene, and to speed up rendering, my team has decided to start using Texture Packer to speed up rendering wherever we can. I have downloaded Texture Packer, packed most of the game's textures onto the image, and exported the atlas. I have also brought in the Texture Packer Unity plugin (free version) into our project. I have attached the TP Mesh Texture Ex script to an object, which includes the TP Helper script. I have selected my atlas and texture that was previously attached to the object before adding TP, as well as making sure the shader is as it used to be. So here is where my problem begins. I have made the new multi-texture png image into a material (import and material settings pictured below) and attached it to one of the plants in the game scene. The texture was made so that the plants were very low poly and used alpha channels to do the details making up the edges of the leaves. When I put the shader on the plant that was on it before (Legacy Shaders/Transparent/Cutout/Diffuse), it does not show the alpha channel (pics below). I need to do this for many different transparent objects in the game scene, so what can I do to fix this issue, or to make textures with an alpha channel packable in the first place?

(Images of relevant settings and examples)

(The original texture before it was put into an atlas)