If the reports are correct about planned changes on tax for transport, HMG will have no trouble identifying vehicle types i.e. Hybrid and PHEV Petrol Diesel Hydrogen etc and thus determine who should use which as such information is part of the vehicles registration. Those vehicles classed as hybrid but not plug in should not need to pay by mile, as all the energy they use still comes solely from petrol or diesel. Plug in hybrids can have a lower pay by mile rate with full EV's having the top rate.
The Plug in hybrids are the odd one out, here becasue its up to the driver to decide if they use the plug in facility or not, and if they don't they would end up paying for fuel duty for all their milage and still be billed for pay by mile. It would almost certainly make business drivers of PHEV's will be encouraged to use the plug in facility to reduce the amount of fossil fuel they use.