Hi Paul ,
Epoxy grout is generally fully chemically resistant, once cured the solvents should have no effect on this grout short term during the saturation period of a solvent impregnator To seal the stone.
The water based should work fine on the stone with the correct saturation but again the epoxy will repel it , you don't need to seal the epoxy grout. I seal with our Eco water based not a problem, still would seal with the Mn solvent if possible like the mpg. (25 years of putting it down, I like the buzz!!! Always use solvent based sensibly and ware a mask. Do not take to Glastonbury !!!
Finally , I didn't think as you did, epoxy would be used surrounding a natural stone tile.
Have had issues with bleed from this type of product before ( long time ago) but again I didn't think it was advised to be used with these products . Ceramics only.? Sure the guys can give us the correct info on this. so i wouldn't ever spec this up!! General natural installation lay- ensure all moisture released , seal, grout generally cementisiouse , again once fully dry impregnate again.