I'm looking at this from the perspective of an add-on; if you're talking an independent mod, much of what I'll say is moot.
For existing mods:
Cloche Call adds the configurable ability to grow trees, plus lots of inter-mod support for the Cloche.
Alfinivia adds support for adding liquids or items as fertilizers to the Cloche, using CraftTweaker.
Based on the Cloche's internals, I suppose it's possible to set certain materials (probably just the "soil" used?) to affect what you grow: from a cursory look you should mainly just need custom IPlantHandler's.
Tier upgrades, on the other hand … no. Forget it. They're just at odds with IE's design. Technically it's possible, but it's not good design. Use Thermal Expansion (specifically, its "Phytogenic Insolator") if you want tier upgrades and such. The Cloche is already very powerful in base IE.