The government's emissions data for a September 2005 registered E500 estate say it is a Euro 3 car. If we look in more detail at the individual limits for Euro 4, it seems that the data on the government site fall within the Euro 4 limits, so it seems the TfL checker is more likely to be correct and the government emissions data is wrong to class the car as euor 3 when the values seem to indicate euro 4 limits are passed. I didn't look at things in a very detailed way, but there does seem to be a discrepancy. As long as TfL is happy, then I would concur that your assessment is reasonable.
per Select a search : Directgov - Car fuel data, CO2 and vehicle tax tools
Manufacturer
MERCEDES-BENZ
Model
E-Class (S211) Estate
Description
E500 (245 Tyres)
Engine capacity
4966
Transmission/gearbox
A7
Fuel type
Petrol
Vehicle tax details
You can pay by Direct Debit for certain vehicles, either annually, six monthly or monthly. Where Direct Debit is available the rates are shown.
Standard rate 12 months
£325.00
Monthly cost: £28.44 – total: £341.25
Standard rate 6 month cost
£178.75
or £170.63 if renewing automatically by Direct Debit
Tax band
K
CO2 emissions (g/km) (weighted)
276
Fuel consumption
Imperial Urban (cold)
16.3
Imperial Extra Urban
33.6
Imperial Combined (weighted)
24.4
Metric Urban (cold)
17.3
Metric Extra Urban
8.4
Metric Combined (weighted)
11.6
Further details
Before using the data here to compare models, please read "how to use the data" in the glossary section
Noise Level [dB(A), moving]
71
CO Emissions
[g/km or mg/km under Euro 5/6]
0.264 ***<1.0g/km per Euro 4***
HC Emissions
[g/km or mg/km under Euro 5/6]
0.044 ***<0.1g/km per Euro 4***
NOx Emissions
[g/km or mg/km under Euro 5/6]
0.016 ***<0.08g/km per Euro 4***
I believe the ULEZ is based on whether the car meets the NOx figure. I put a Y plate CL500's reg in and it's ok. That said, by the time the N/S circ extension is running I wouldn't be surprised if they have turned the screw and you need a Euro 5 or whatever. I wouldn't buy a car because of it yet.