I just updated my personal Pack to Pixelmon 7.0.3 and noticed an issue with your mod.
I wasn't able to plant any slime saplings from Tinker's Construct in Bonsai Pots from Bonsai Trees.

I copied the config files from your jar to the default minecraft config folder and deleted the bonsaitrees folder in the assets folde afterwards. That worked out.

Tested with:
(Working)

• Minecraft 1.12.2
• Forge 2768
• Bonsai Trees 1.12-b144
• Mantle 1.3.3.42
• Tinker's Contruct 1.12.2-2.12.0.115

(Not Working)

• Pixelmon 7.0.3
• Apricorn Tree Farm 1.12.2-2.0.4

I don't know if other mods affected by this, vanilla saplings worked though.

If that's the case, then I'll remove Bonsai Trees compatibility and upload the config files as a separate zip file.

Thanks. I guess directly submitting a PR with the files to Bonsai Trees wouldn't be downward compatible with Pixelmon. So I can't think of any other solution.

Edit:
Although, since you don't have the files for the Pixelmon 6 version, it might be be worth submitting that PR. Then it would always require the latest versions of the mods. And maybe you can provide extra files for version 6. I believe that would be an alternative, since the extra files should have a higher priority. But I'm not sure about that.

@BeetoGuy The issue still exists in the 2.0.5 update. There are still bonsai trees related folders in the assets folder of the jar.