Yes, LDPE Nalgene do not leach much of anything that is detectable at the molecular level. Should be inert and stable enough for storage, short or long term. Depending on your pocket book. I really just thought they would be great for EDC. Not like you would need many so the cost would be absorbable over the long haul.
As for the "bloom". It does not sound like the bloom that is desired is fungal in nature. Or at least not from what I can tell from the discussion. It seems analogous to sap moving to the surface in heartwood or sapwood.
What is probably happening is that after the tobacco is cut and dried under heat and pressure, the sugars crystallize in place. But with changes in humidity and/or temperature, these sugars may change states, temporarily moving from crystal form back to sap/semi-liquid form and since the tobacco was compressed into cakes under pressure, it moves to the surface where the pressure is less and it recrystallizes or forms a crust.