For the two sides that said the Good/Neutral or the Bad Ending were the true endings (me believing the Good Ending was the true ending), none of us were right. I personally, in my explanation as to why the Good Ending was the true ending, said that we the player were involved in the story...and that part is true, but not during the ending sequence of stopping Vanessa (helping PAFF or otherwise). I believe the player is the E00200 that Violette mentioned, but, even if that isn't the case, we are still involved in the story. During the version 4.0 ending sequence, it shows PAFF and Corrupted-Vanessa talking to somebody, this somebody being referred to as "You", meaning us the player. PAFF and Corrupted-Vanessa reveals to us that we have been spectating the entire time via the OA/OS space since our physical body in the real world has been in a coma for about 10 years and, since we have the Eye of Horus ability like PAFF and Nora, our power has grown quite powerful over that time. The three endings we could potentially unlock in version 3.0...never happened. Not the Good, Neutral or Bad Ending(s).
The PAFF and Corrupted-Vanessa speaking to you aren't the real ones, they're digitalized versions of themselves created by you...their sole purpose is to help you realize the truth of your current state (since, as they reveal to you, you've been in your digital consciousness for so long that you've forgotten your memories and lost most of your emotions) and to realize the gravity of the situation you've been witnessing from the sidelines. The three endings you could have received in the 3.0 version are your perceived possibilities: if you help PAFF stop Vanessa from releasing the Ender virus, then humanity will be saved but at the cost of killing an android that was as pure as can be and didn't want to harm humans, but got overwhelmed by her negative emotions; if you decide not to reach out to PAFF, she will face Vanessa alone, potentially succeed in stopping her, but will die with Vanessa due to the strain on her body...humanity will survive nonetheless due to one human girl's sacrifice; finally, if you decide not to reach out to PAFF and she potentially fails to stop Vanessa due to her hesitation, the Ender virus will successfully be released and all humans will be eradicated (but potentially you, PAFF and Nora due to your immunities to the virus, all three of you likely dying via other means). PAFF and Corrupted-Vanessa notify you that none of these have come to pass...yet, and tell you only you can make the decision, they won't force a decision onto you, and whatever you decide will be the "New Beginning". The final nail in the coffin that the entirety of the game was you spectating from the sidelines and the endings from 3.0 are simulations based on your perceived calculations of what could happen is the new timeline mechanic that was added in the latest version. When you open The New Beginning tab at the end of the timeline, there are no files that contain the three potential endings. The last file in the timeline is you attempting to approach an anguished, sobbing Vanessa right after Ivy was shot and killed, and the "fake" PAFF and Corrupted-Vanessa confronting you before you could come into contact with Vanessa, warning you that making contact with her now could cause you harm due to her being overwhelmed by her negative emotions after witnessing Ivy's demise.
Granted, I admittedly have yet to see if the timeline changes after I try to do any of the three endings after 4.0's update, so I don't know if it changes do to the ending you choose nor if there's any easter eggs after having your conversation with PAFF and Corrupted-Vanessa and obtaining an ending. May update this after my phone charges and I unlock all three endings during the version 4.0 update.