A much shorter tunnel, but with two new underground train stations, is being built under Stockholm, Sweden.[1] It is about 1/6 of the Swiss budget (about $2 billion). It will be completed on budget and slightly ahead of time this year.[2] So it can be done.
Indeed projects in Sweden run över budget too. I was saying "it can be done" not that it is always successful. Other recent successes:
Norra länken 2.6 Bn SEK under budget (part of circle road around Stockholm). [1][2] Arlandabanan (train service to Stockholm AirPort), on time and on budget. [3]
One involves carving a 150km tunnel through a granite massif which is the Alps in a scale that never before was done in history of mankind, the other involves drilling a tunnel through alluvium and sedimentary deposits pretty much like any medium-scale tunneling work.
[1] https://en.m.wikipedia.org/wiki/Stockholm_City_Line
[2] in Swedish. http://framtidensinfrastruktur.se/artikel/snart-fardigbyggt-...