Crossrail is the 4th most costly 'megaproject' involving transport both under construction and 4th including all completed projects. There isn't any way to look at it where it isn't one of the world's largest construction projects unless you start looking at space stations and if cities were 'megaprojects'
It wasn't mentioned that it will cost 25 billion - which btw is a ridicilous high number in comparison to other tunnel projects.
Also for example the Gotthard base tunnel or the Brenner base tunnel are longer and therefor 'larger' then those described in the article.
Even looking at Gotthard tunnel is rather bad because it's just a tunnel though in very difficult conditions and large as you say is a bad comparison against a new railway network under a densely populated city.
Crossrail is large in the context it has new stations, depots, extensions, trains, and the very large amount of traffic it is expected to take under a very short construction period.
Looking at the entire picture doesn't make the number seem ridiculously high. If it seems to high you need to look at where it's all going its not just for a tunnel.
Crossrail is at 100 million working hours so far, with 10,000 people working across over 40 construction sites, according to http://www.crossrail.co.uk/news/crossrail-in-numbers (which also describes it as "Europe's largest construction project").
Longer and deeper, sure, but Crossrail is a whole other level of complexity due to being built under of one of the world's largest and most congested cities.
[1] https://en.wikipedia.org/wiki/List_of_transport_megaprojects