Unfortunately strictly speaking TFL hold all the cards here so for petrol as that's what we're talking about if TFL were only sticking rigid to the Euro 4 limits with no single vehicle exemption then no zed 3 would be ok as Euro 4 is around 2006 on even Euro 3 is 2001 on.
So as you know certain early cars can get an exemption if clean enough
Now i know there are 2.2 and 3.0 zeds with exemptions now if they are refusing yours i may know why
I have done mot on 2 different customers in different depot ( each more than once) so know both cars
One is a 2000 3.0
The other is a 2001 3.0 model
There is a big difference between them and that is the exhaust.
The early car has the same exhaust as my 2.8 tu so something like this with 2 underneath cats and single pipe into rear box
Then the later one has 4 cats primary and secondary and twin pipes into rear box
Now i am going to imagine these are the ones with the exemption for it .
If yours is the later style it may be worth trying to find other 3.0 owners to use as a precedent set.
But need to make sure yours is the later one or it probably doesn't run clean enough.
Stephen.