Failing to review transcripts is substandard practice: serious fault in the DA there. However, unless significant allegations in the transcript are absent from the statement, it's unlikely to resolve the statement's contradiction of a crime.

A confident claim is not a conclusive legal determination drawn from alleged facts. According to the reported transcript, she was confident about the statement, too:

On the second day of the interview, Jane Doe reviewed the revised six-page statement. The transcript shows her adviser asked if she wanted her and another adviser to review the statement.

Before signing, the transcript shows Jane Doe said, "I'm very confident about this."

When the only allegation recommending a criminal charge alleges facts that not only fail to support that conclusion but negate key statutory elements of the crime, that eliminates every prosecutable theory and legal basis for an investigation. Such a contradiction is not resolvable through further investigation. At least some plausible basis for a crime needs to be articulated for an investigation to justifiably proceed.

The DA gave the complainant notice of his determination and an opportunity to review it together. That was another chance to raise any allegations the DA could have missed & explain how they arrived to their conclusion when alleged facts reviewed so far didn't support it. The complainant apparently waived the opportunity.

The "multiple things indicating lack of consent" are worse than you wrote, yet they don't satisfy the element of the crime. A feeling lacking clear expression is not a fact supporting the legal standard; she had the liberty to reject, exercised it, and was met with compliance

According to the statement, each time Jane Doe asked to stop the sexual conduct, the sexual conduct stopped.

Shutting down events and distasteful language in snapchat obviously don't qualify.

Much that you mention or that comes up in these stories is already in the statement, too. Some allegation that actually meets the legal standards is needed.

This is an issue with a lot of these kinds of cases (where a lot of drinking and drugs are involved). Based on the summary of her statements, the first two guys she willingly hooked up with were probably too intoxicated to consent by most people's standards. One passed out basically during sex and the other was dry heaving/throwing up shortly after.

At the end of the day, the biggest issue is you're going to struggle to convince a jury beyond a reasonable doubt that any person's story is reliable.

Under New York State Law, “mental incapacitation” occurs when a victim is rendered incapable of controlling her own conduct due to the administration of a drug without her consent. The facts provided by Jane Doe’s statement do not allege that she was either rendered incapable of controlling her own conduct or that any drug was administered to her without her consent.

She alleged cognitive capacity (understood what she's doing), volition (willing choices), not incapacity to control her conduct, compulsion, inability to communicate willingness, expression of nonconsent, etc. Throughout the recollection, she was understanding, rejecting & accepting requests, choosing offers, conducting choices. She exercised autonomy.

The legal standard of "mental incapacitation" isn't an incapacity to recall, it's an incapacity to control one's own actions (with conditions). Memory‑formation failure is not a loss of volitional control. People are still responsive to stimuli, can have full on conversations, can conduct willful choices. Their failure to recall it later is retrospective. That does not mean people weren't cognizant at the time and making willful choices. The law doesn't say black-out drunks lack a choice when they commit a crime. Dumber, less inhibited choices aren't a lack of willing choice.

I doubt the structure of the law & its standards would support your suggested interpretation of "mental incapacitation". It explicitly rejects voluntary intoxication, and she alleges legally significant capacity to understand & choose her conduct. New York already rejects intoxication as a defense for criminal liability. Consistency with that is unlikely to support constructions for consensual intoxication as a substantial incapacity to understand and control one's own conduct (which would excuse liability).

But if the law does that, I assume the law would take into account the intoxication levels of the men too? Or you might not have thought this all the way through?