Yes, I removed the broken recipes for all of the gardens.
Unfortunately Pyanodon's mods seem to just chuck all of the recipes into a few giant umbrella technologies like "Coal Processing" instead of organizing the items into an actual tech tree, leading to often having things unlocked that you cant craft. Thankfully most other mods are better about this.
The two versions of the same item are caused by both mods adding their own separate version. The compatibility patch mod I've included in the pack takes care of most of these problems, but doesn't actually remove the overlapping items, since other mods could possibly try to use them afterwards and crash, so you can still see them in FNEI.
The only way to fix these problems definitively would be to go through each and every item, recipe, and tech in all of the mods and create a unified mod that requires all of them and adds, removes, patches, and reorganizes everything to be seamlessly compatible. This would be a ton of work, and I just don't have the time to do this currently. For now, I'm trying to avoid large reworks and just allow the mods to be used together, however I am planning on developing a modpack of this sort in the future, and have already laid some of the required groundwork :)