Telling a manager "we uncovered work that wasn't in the original spec" isn't literally the same thing as telling them they aren't doing their job.
In a situation like that, you can recover, but it requires tact. The end of this story was that they left the company. An alternate ending is that they may have been let go.
If they’re paying you to work on a doomed project, you have to work on it, or change it. And if you want to change it, political maneuvering is necessary.
But what's their incentive? They're probably paid as a regular IC, and saving a double-digit million dollar fiasco like this from disaster is super annoying and unrewarding work! You're effectively doing the job of five managers and not even getting their salary -- let alone a percentage of the disaster you're averting! This kind of political-technical skill combination can probably be fruitfully applied in a place that properly rewards the contributor!
I very much agree that this thing could have been handled better, when seen externally. But I'm also pretty sure it wasn't in OP's personal interest to do so! That's a very stupid state of affairs, of course, but I guess that might be par for the course of a failed $60 million project.
I'd bet it doesnt requires tact to convince them anymore.
If necessary someone else will tell them they are not doing there job. Stick to your role.
Pointing out that you've underestimated by X is pointing out something everyone already knows. And advocating to blow up the estimate by X so early in the project is arguing to piss the customer off and possibly walk away from $60 million. That's why everyone patted them on the head and blew them off. Everyone else understood the game but it's a bit gauche for them to explicitly explain what's going on.