Why do you think the boiler transformer is only 16 volts?

Must have primary stage to thermostat not wired correctly. If supply voltage is 208v make sure your on the 208v wire if your on the 240v with 208v supply you secondary will be low. But i don't think all the components on the boiler are 16v coil I think your reading low secondary supply voltage due to incorrect wiring on primary to transformer