Firstly, "unrecognizable plate" simply means the automated system couldn't read the plate. In cases such as this they use an actual human to read the plate, They can blow up the pic to assist in this.
As for the comment they "let him steal rides". Do you expect them to monitor it EVERY hour of every day? I suspect the "system"merely kicks out unrecognizable plates perhaps once per month then they have to look at it to determine, the plate.
It sounds like, (from the OP's post), like they got the plate right, (his friend didn't deny using the road), merely is now looking to get a "special deal". He is stuck in a catch 22 ignore the bill and don't acknowledge ANY form of use, (BUT at plate renewal time he will be screwed), or go in and discuss a payment plan, (at which point he has acknowledged his use of the road).
They may or may not play ball. At VERY least he should request to pay ONLY the actual tolls and have them eat the interest and penalties, (which they are likely to do, UNLESS the photos make it clear he was trying to evade the toll charges.