Thing is with Magical Crops and Bees with your pack idea (no ore gen), where is the player going to get the resources to get started? You need a diamond, 4 of the "ore drops/ingots" (and various amounts of essence) to make your first seed. Bees need machines to process the bee materials.
With no ores in world gen (and assume no Ex Nilo), players are limited to dungeons, oreberries (boo, hiss for removing them TiC!) and mob drops. Dungeons will be the best bet (especially modded dungeons like Better Dungeons), but the player will be using Stone and Leather equipment, those dungeons will be difficult.
With magical crops, if you disable the essence ore being generated, players can only get essence from the plants, they are going to need a massive farm of them. But, when you automate Magical Crops with MFR, you don't get the secondary drops from the crops, which actually reduces your output of raw essence. It's better to manually harvest the essence plants (or build a water piston harvest system), and use MFR on the seeds you've made.
To be able to automate the player needs resources and energy generation they won't have. They will be manually farming and dungeon hunting for a long while before anything can be automated.
With Ex Nilo alone, I think the best possible balance is for non-automated sieving, producing only Copper/Tin/Iron (early game resources which exist as Ore Berries (which are the same as a magical crop 0% seed plant...)). Since I'm not aware of any other mod that can produce the other resources in any great useful number "early game", the remaining resources would have to remain as world gen which you harvest with materials from your sieving/ore berries.
Another idea, that is semi evil that I use, is to add SilverFish veins into the world generation, and using Father Toast Mob properties, have them have a chance at dropping random dusts. Players will be able to get some resources, and eventually in time, use MFR to mob spawn and grind them.
