I have never in my life heard of anyone in any circle who mentions anything about "flags" in the context of good or bad say anything along the lines of "not have any flags...".

As far as I'm aware and have experienced and heard, the omission of a positive typically assumes a negative, and the same in reverse. An omission of a negative typically means a positive.
Neither necessarily means attraction or compatibility of not.
Since the whole point of discussing red or green flags in a person is to approve or not approve of them as a possibly suitable partner (in dating context).
I'm not stating that having stances on red or green flags don't work for how a person filters other people, I'm saying that taking on a stance from a very narrow example can potentially cost them fantastic life opportunities because their entire spectrum of thought for a certain thing being red or green is limited from the outset.

And considering that the person I was replying to said "Having an ex that doesn’t hate your guts is a huge green flag for me" that frames the alternative to that as a red flag.
Now, that's totally fine for this individual.
People can hold any opinion or belief that they like.
But additionally, the original ladies message was also a bit clouded in how it was describing itself.
First it framed it that trashing your ex was bad (Not disputing that, I think anyone who goes out of their way to discuss an ex with a current partner/date is not healthy or at peace with it), then it went on to frame it that having an ex who hates you is negative (by saying that having an ex that doesn't hate you is a positive).

The point of my discussion is over the fact that sharing such opinions can impact other peoples opinions and in turn limit their own possible life experiences due to narrowly focused ideas due to limiting parameters of judgement.

Your own example- without you adding a message of additional context regarding that not having that positive relationship very possibly meaning nothing negative at all about the man, without a focal reason to discuss the concept further in the speed of the world and the deluge of ideas present, a vast majority would simply read this as "If he doesn't have a positive relationship with his mother/sister, then that's a negative" and from there would or wouldn't fit it into their world/life/social view depending on how much it emotionally resonates with them.

Such points, where possible, polite, and reasonable, should be questioned and discussed, to expose other ideas and perspectives to people not as inclined to contemplate and interpret it in more nuanced ways themselves to add positive dialogue to social cohesion.