You can use aluminum flex vent pipe connectors for water heater venting if they are approved in your local jurisdiction, and if they are Listed (Approved) for this particular type of installation.
Things start deviating from “normal” when people who don’t know much and don’t care (because they don’t have to or need to) about types of material that can be used for water heater vent pipe perform installations themselves.
Details like thickness of the vent pipe material, its type and form (solid / corrugated), listed or not listed seem to have no meaning; aluminum is aluminum, it doesn’t matter that somebody put a label on it listing it suitable for a clothes dryer venting only. I guess I made it easier for myself by simplifying the requirement in my post and avoiding questions?… up until now.
You can find most of the regulations at the following links below.
There’s a bit more in NFPA 211 (publication is not freely available) that adds a paragraph about using corrugated vent pipes and requires them to be LISTED for the particular purpose. So, if the label on a flexible aluminum vent connector says that the connector is Listed for venting of natural draft water heaters, the next step would be to verify with local authorities if the code adopted in your jurisdiction permits such use. It may sometimes not allow it at all or there could be exceptions from using the connector in certain areas / locations (single wall or double wall conectors).
Two citations from the links listed above:
IMC (International Mechanical Code)
803.8 Vent connector construction. Vent connectors shall be constructed of metal. The minimum thickness of the connector shall be 0.0136 inch (0.345 mm) (No. 28 gage) for galvanized steel, 0.022 inch (0.6 mm) (No. 26 B & S gage) for copper, and 0.020 inch (0.5 mm) (No. 24 B & S gage) for aluminum.
IFGC (International Fuel Gas Code)
503.10.2.1 General. A vent connector shall be made of noncombustible corrosion-resistant material capable of withstanding the vent gas temperature produced by the appliance and of sufficient thickness to withstand physical damage.
503.10.2.3 Residential-type appliance connectors. Where vent connectors for residential-type appliances are not installed in attics or other unconditioned spaces, connectors for listed appliances having draft hoods, appliances having draft hoods and equipped with listed conversion burners and Category I appliances shall be one of the following:
1. Type B or L vent material;
2. Galvanized sheet steel not less than 0.018 inch (0.46 mm) thick;
3. Aluminum (1100 or 3003 alloy or equivalent) sheet not less than 0.027 inch (0.69 mm) thick;
4. Stainless steel sheet not less than 0.012 inch (0.31 mm) thick;
5. Smooth interior wall metal pipe having resistance to heat and corrosion equal to or greater than that of Item 2, 3 or 4 above; or
6. A listed vent connector.
Vent connectors shall not be covered with insulation.
Exception: Listed insulated vent connectors shall be installed in accordance with the manufacturer's installation instructions.