This gives an interesting insight into the operational costs of an electric train vs for instance a car. The fuel cost is a far higher proportion of the cost of a mile than for the other costs presuming you own the car, it is only really road tax and MOT.
But in the case of the rail industry, the cost of the asset is also appropriate. In my case, at an average of 95mpg and 17mpkWh, fuel/electricity account for 7p per mile, but when the cost of finance against expected usage is included it's 44p. Add insurance and tax and it's 52p. The same will be true of the railway, the cost of the asset itself, along with driver & guard labour, stock maintenance etc. will be the bulk of the cost, not the raw per mile costs.
More on-topic, that updated comparison is more like what I'd expect, the 769s are heavier than the 319s but they aren't that much heavier, a slight increase seems proportionate - the much heavier PMS on Mk3 EMUs is always going to up the track access charge compared to short vehicle length DMUs with evenly distributed equipment. Heavier DMUs like 185s, however, I wouldn't expect to fare so well, and likewise I'd expect modern lightweight EMUs to fare better, also in part due to their lower power usage per vehicle km.