I have a feeling it should work for the protected 3vs because he's not offering a separate charger for those.
When I ordered my 3v protected batteries for the Thermo from an eBay seller, a charger was part of the deal. So I'll have 2 chargers to possibly to work with the 16340 batteries but of course I don't want to kil anything if protected or unprotected batteries need different chargers.
Good question because I can't manage anymore chargers..I already have one for my NIMH camera batteries, I have the TR-001 for my 14500's and 14650's and now I'm getting one with the 16340's pretty soon I will need a separate power strip just for these chargers =/

well good i'm glad it was moved