I suspect what he means is that because they are supposedly registered in the EU, but in a different member state than the customer, they should be able to accept the VAT registration number of the customer and charge net - the VAT is deducted at source.
But, presumably, they aren't doing this. And if they don't, it complicates reclaiming the VAT - you can't deduct VAT from a different member state on your UK VAT return; only UK VAT charged at the UK rates.