The counterpoint is valid (rising seas don't help), but then we have Saint Petersburg ([1]) that's literally build on top of swamps and occupies multiple islands. It has a first class subway ([2]). It's a little deeper than regular subways, but it exists and works really well.
Forget the tunnels, sealing those is commonplace, what really matters is the station entrances. St. Petersburg station entrances were built well above sea level, and by "sea level" I mean the level the builders expected for the foreseeable future.