Aight, I usually try not to engage, but let's look at this.
The things the factions mostly provide is political and economic support. The players are the muscle. If they didn't need to tell them to get more economic support then why should they?
If the players are the muscle of a faction, they're still a part of the faction. Most organizations need the different chambers of it to communicate to function. For example, a military unit cannot just go and fight another army without confirmation from the leadership.
Not saying the Harpers or the others are like this - in my game, the Harpers specifically betted that my players would act like the mercenaries they are and only lightly nudge them in the right direction. It's callous, but also much less risky. The Harpers assume that the party will try and go at it alone, but being Good aligned, will send a rescue party anyway - to perhaps secure some or all of the gold themselves, but mostly to get Manshoon to leave Waterdeep.
There is simply no way, for example, that the doom raiders just let the players keep the gold... why the hell would they?
You had not chance to know this, but one of my players have a familial connection to Davil, and has made overtures to mend a rivalry with Tashlyn. She's informed the remaining Raiders that she is close to foiling Manshoon, and they want to help. If they learn of the gold they'll likely want it for themselves, but since my Raider player has been good at being nice with them, they'll decide to call it quits if the players roll well enough of Persuasion/Intimidation.
And the harpers are so riddled with Zhent spies that telling them something might as well be telling it to Manshoon.
I guess that's possible, but it isn't in the book, so I didn't really implement that. Not a great reason for keeping the gold and info about it for themselves, however.
I guess I don't see the reasoning behind throwing a CR 13-14 bbeg + his top lieutenants because you think them keeping secrets is weird (when it's not). All the source material I've ever read on it suggests sending raiding parties led by a lieutenant or two not sending the BBEG themself. If anything you should have some fucking self-control and not reach for the BBEG.
It's the books approach - if Manshoon is the villain, his Simulacrum (CR 8), Vevette (CR 3), Agorn (CR 2) and three Thugs arrive to stop them as the party leave the Vault. Then, allies arrive to help them when things get dire. It's a bit rough for sure, but I think it fits with the theme of the book - the players are underdogs, and will get more out of choosing to work with a faction or individuals like Renaer than trying to go at it themselves.
Also, the book states that no faction will allow the players to keep all the gold once it surfaces that they have it - eventually, they will be arrested or forced out of Waterdeep. I think that also plays into the theme.
The players had the self-control to not brown-nose and beg Vajra, Laeral, and Hlam into doing all the work for them so I think you should be able to manage not dropping the BBEG equivalent at the 11th hour.
Well that isn't necessary; they could just inform their allies, like their allies have done countless times. My players have had their asses saved multiple times and have come to expect the factions to do so - but if the factions don't know they need saving, how can they come to help out?
And, It seems like that's a fight that can only be won by DM intervention (which is what you're planning). That is just so fucking lame. It just sounds like you're but-hurt that they're not playing with your DMPC, or something, so you're going to create a deus ex machina situation and force them to sit through it right at the end of the game.
Again, that's how the book is written. To flip it around, I think it would be quite dry if the campaign is decided by a straight decently-winnable fight. Something has to connect to the themes of the book and our campaign, which is that Factions are in control of Waterdeep, and aligning yourself with them is often a good idea, and that greed is bad; especially when so many powerful groups are gunning for it.
I think the book is going for a "With Friends like these", Avengers Endgame sort of moment where all the allies the players made come to help them, which I think is really cool.
Just the clarify, I have changed loads about how the book has run the game, but I do want to stick somewhat to the material, because I do really like it.
Horrible DM decision.
Alright.