As long as it says "100% silicone", you're safe. I don't see how any pigmented or colored silicone could be 100%, it may be safem but why take chance.
Seems like coating a pipe with caulking could be a messy chore, be sure and wear gloves, getting silicone off hands is another chore. Have you given thought to using epoxy? There are some that state they are "aquarium safe" though reading ingredients of some non labeled ones shows no diff.
The resins used for fiberglass tanks usually say safe for potable water, you can brush that onto pipes then coat in sand.