I don't really see how that rules out Perfect Dark. Phil said The Initiative was doing "new things and old things in new ways". As I see it, that can be taken one of 2 ways:

1. The Initiative actually has 2 games in development, 1 a new IP (new things), the other a revival of a dormant IP (old things in new ways)

2. The Initiative only has 1 game in development. In this scenario, "New things" could match with the rumors we've heard of Perfect Dark reboot having an unprecedented shared world design that lets multiple players compete against each other to finish story driven spy missions first. "Old things in new ways" could very easily describe a reboot of an old IP. The single game scenario could also be used to describe a new IP, but saying "old things in new ways" kind of kills the possibility of it being a new IP, unless "old things in new ways" refers to a new take on an existing game genre, rather than to the IP itself. 

And then of course you have Phil in the E3 2018 interview when The Initiative first opened saying that one of the first things he did after The Initiative was created, was show studio head Darrel Gallagher a portfolio of IP's that MS owns, with Phil straight up saying in the interview that one of those dormant IP interested Darrel, clearly teasing that The Initiative planned to reboot that IP. Out of the whole portfolio of IP's that MS owns, Perfect Dark makes the most sense to be the IP Darrel was interested in, as there are alot of similarities between Perfect Dark and Tomb Raider (which Darrel previously successfully rebooted), both being 5th gen games with female playable characters praised for their sex appeal, and credited with creating many new female gamers at the time. 

Sex appeal was definitely a focus of Joanna's design and marketing:

Perfect Dark commercial where Joanna was portrayed by American Model Michelle Merkin, who made Maxim's Hot 100 several years)

Sex appeal was definitely a focus of Joanna's design and marketing:

Perfect Dark commercial where Joanna was portrayed by American Model Michelle Merkin, who made Maxim's Hot 100 several years

N64 US and EU boxarts where Joanna's face is shown with make-up applied

Magazine cover for Perfect Dark with exposed cleavagePrima Games Strategy Guide cover showing Joanna in a skin tight, sexy outfit

Japan Strategy Guide cover

This is from the reception section of Joanna's Wikipedia article:

Joanna Dark is among Rare's most well known characters. In 2007, Tom's Games included her on the list of the 50 greatest female characters in video game history, calling her "all three Charlie's Angels rolled into one" and stating she should be played by Jessica Biel.^[13] In 2008, Spike featured Joanna Dark as sixth on their list of "The Top Video Game Vixens",^[14] and The Age ranked her as the 20th greatest Xbox character of all time even as her Perfect Dark Zero "may not have been the greatest entry for" her as opposed to the first game for the Nintendo consoles.^[15] In 2013, Scott Marley of Daily Record ranked her as the third most attractive female video game character.^[16] In 2015, Thanh Niên ranked this "perfect spy" as the fifth most sexy female video game character.^[17] Entertainment Weekly elected Joanna Dark the 14th coolest videogame character, adding "[w]hen James Bond goes to sleep, he dreams of being Joanna Dark."^[18]

Sex appeal was very difficult to portray on 5th gen hardware, 3D graphics were still in their infancy and many attempts to make characters look sexy in-game failed miserably, I think that is why there was the disconnect between the game and the marketing. Look at some "sexy" 5th gen game characters, they are absolutely horrific, nightmare inducing:

I'm pretty sure I remember reading an interview where Rare said they wanted to make her sexier in-game, but felt it wasn't possible due to limitations on N64. 

Turn 10 spent a lot of that time reworking the engine, Forza Motorsport 8 only entered the "concept phase" on March 8th, 2019, they also mentioned they want the public to be involved in the development and we've seen zero of that so far, unless they changed their minds.