Behlen sealer is water based in that it cleans up with water. Once its dry... its like a rock.
If you're using an oil based stain, there should be no problem over grain filler of water or oil base. I'd not "sanding seal" the wood before staining, as that will prohibit the stain from entering the wood. Grain filler is to level the surface, the deep pores fill in, but you sand it back so there is still much exposed wood to accept the stain.
Oil based fillers work well too.. but take a long time to dry. Water base takes 2-4 hours. Oil... 2-4 days. I see no advantage to oil based filler, as the water based filler is compatible with everything from pure tung oil to nitro lacquer