I use about 70,000 litres of diesel per year in my truck. The money would have to come from somewhere. I don't think the government would implement a rebate scheme as it's open to abuse/fraud and if the only other way to absorb the cost is to pass it on to the customer then you know what that means as we are the customers at the end of the chain.
When the Lorry Road User Charge (LRUC) was planned the idea was that every truck in the UK would be fitted with a GPS tracker. this included all the foreign trucks on entry into the UK too. As they clocked up the miles they would be billed as a way of getting some revenue from Johnny foreigner. For UK based trucks, it would have been cost neutral as all the fees would be netted off against fuel tax. If Johnny Foreigner decided to buy fuel in the UK they could off set some too. Many would just have to pay the bill though as they just filled up in Luxemborg did all of their UK work and back to Lux to fill up with cheap fuel. It was these ones that they were trying to get some money out of as otherwise the UK government got nothing.
In the end LRUC was dropped as the infrastructure to set it up was going to cost billions (I was involved in the bidding process for one company) and the payback period was too long.
For VED its much simpler. Lets say you have an average car that does 45mpg. The average car tax is £130 and the average mileage is 10,000 per year. You need to add just under 13p/litre to recoup that.
You have a truck that you currently pay (lets say) £1000 a year in VED for. You use 70,000 litres a year so you will pay £9,000 extra for fuel but you just put your claim in each month or year to claim back 11p/litre meaning you are back to where you started. No worse off and simple to do.
The ones it wont get to pay into the system still are the ones that fill up in Lux with enough fuel to run around the UK for a week before heading back across the channel. Under EU rules we cant charge them a tax on entry/exit but come 2019, if we want the EU to start reciprocating, we could.