Thaumic bees don't add recipe for apatite, they allow to use it more efficiently by making concentrated compound. The only options seem to be either GT (chemical reactor or centrifuging soul sand from alkhestry) or RC saltpeter.
However apatite spawns are so large and can be used with fortune and farms use really small amounts of fertilizer, that in normal play you will probably never run out of it.
Edit: There will be some changes in 1.5 forestry, nerfing other tree cutting methods:
"Sapling yield in the fermenter has changed. The amount of biomass produced from a single sapling is now determined by the sappiness trait on it. Saplings without genetic information are treated as though they have lowest sappiness. Average sappiness boosts biomass yield back to the previous level. High sappiness increases it to 150 % of the previous yield."
However apatite spawns are so large and can be used with fortune and farms use really small amounts of fertilizer, that in normal play you will probably never run out of it.
Edit: There will be some changes in 1.5 forestry, nerfing other tree cutting methods:
"Sapling yield in the fermenter has changed. The amount of biomass produced from a single sapling is now determined by the sappiness trait on it. Saplings without genetic information are treated as though they have lowest sappiness. Average sappiness boosts biomass yield back to the previous level. High sappiness increases it to 150 % of the previous yield."