There will indeed be no emissions in battery mode, but in diesel mode there will be EXTRA emissions in order to produce the energy used to charge the battery.
A reduction of 25% in fuel consumption and therefore also a reduction of 25% in carbon dioxide emissions is a relatively small reduction if compared to the use of an electric train. (battery powered or OHLE powered)
Surely it depends on how much of the battery charging is from regeneration on braking - likely to be a greater proportion on suburban services with many stops? So not all of that battery power has resulted in extra emissions.
And the comparison with electric needs to recognise that there is still a carbon footprint with electric, so a 25% saving is a greater proportion of potential saving you would get if the service was electrified. (eg, if a fully electric service resulted in a reduction in carbon emissions of 80%, then the proportionate saving of the hybrid approach is 25/80 =31%).
If you can get that sort of saving in a couple of years from modifying existing rolling stock that sounds like a no-brainer given the costs and timescales involved in a large scale electrification programme (assuming the trains have a long enough expected life to make it financially viable).
There's also the improvement in local air quality and noise to consider too, apparently a big issue at Marylebone. At the places where it is likely to be an issue, you get more or less the full benefit of electrification with this solution.