Yes I agree that there wouldn't be the stomach for two new rail tunnels. But to be fair, the intercity tunnel wouldn't just be for the benefit of people travelling from Québec. It would also serve all of the northern and eastern suburbs via the St Jérôme line, and Mascouche Line, respectively, as well as the VIA long-distance services from Jonquière and Senneterre (and more importantly, Shawinigan and Joliette). And as drawn, it would also serve the western lines (Vaudreuil-Dorion and Candiac), providing them with a new connection to the various services using Gare Centrale (REM, VIA, Amtrak and other Exo Lines).
If the tunnel were to be funded by the City of Montréal, then certainly they would choose a metro over an intercity line. But large infrastructure projects like either of those are typically funded mostly by the province and feds, so the fact that the benefits are spread across the province is actually a point in favour of a mainline rail tunnel.