Phyrexia and Black mana
As much as this man was an entitled incel, he still believed in a specific philosophy.
Phyrexia in MTG has been tied overtly to Black mana. In old flavor all phyrexians were black aligned (barring a few errata’d ones) and even by the time of New Phyrexia, when Phyrexia had access to all colours, it is still predominantly in Black (though in Scars of Mirrodin Green was framed as the second most phyrexian color, and an All Will be One and March of the Machine White has essentially become the de facto phyrexian color after Black).
A lot of this essentially boils down to three things: “elemental” aspects of the color pie, old villains being mostly Black, and marketing.
Is Phyrexia a Black system/philosophy?
I’d argue no, not really. “Progressive evolution” as Phyresis means simply means acquiring perfection through mettalurgy (Blue) and eugenics through survival of the fittest (Green). Both new and Old Phyrexia had strict religious hierarchies and scriptures, so White always felt at home. Overally, I’d see Phyrexia as a civilisation as a dark take on Bant, which seems to be the direction New Phyrexia under Elesh Norn is heading.
Now, Yawgmoth WAS Black aligned. The Thran throughly depicts him as an entitled, narcissistic freak, and you can argue that by the later stages of the Weatherlight Saga he abandoned all philosophy for the sake of petty revenge. But given his philosophy at least in The Thran, there’s an argument to be made that he is Sultai, since he does believe in phyresis in its eugenicist purpose.
Ultimately, Old Phyrexia was mono-Black simply as an extension of Yawgmoth, and even then I’d argue other colours were present. The pneumagogs, for example, were pretty white aligned.
The elemental reason
MTG may have complex philosophies, but often things are of a certain colour just because that color controls an element. This is why you often hear of “wet blue” among the vorthos, where giant creatures better fitting in Green are mono-Blue due to being aquatic.
Phyrexia is matter of factly an undead faction. Phyresis destroys the body and implicitly the soul (though the Pneumagogs and Jin-Gitaxias experiments show that the soul can be preserved), so a compleated being is always brought back as a husk via necromancy. Black is the colour of necromantic magic, so it makes sense Phyrexia is Black aligned due to that.
However, other colours have steadily have had necromancy. Best seen is in the Lorehold College of Strixhaven, where spirits are ressurected, the mummies of Amonkhet which are mostly white aligned (albeit thanks to some curating and embalming) and the various Blue zombies we’ve had since Innistrad. Both Green and White have ressurection mechanics, so it’s not out of flavor to depict them as engaging in necromancy, albeit perhaps a more “bring back to life” style than Black’s puppet style.
Thus, while the elemental aspect probably means phyrexians will always be at home in Black, other colours can do it too.
During the late 90's/early 2000’s, MTG banned demons due to evengalist protests. The satanic scare wasn’t satisfied with Pokemon or Harry Potter, so even an innocent card game had to pay. On the plus side, we’ve gotten quite a biting satire in the form of the Church of Tal.
To replace demons, horrors became Black’s iconics, replacing the satanic with the lovecraftian. And Phyrexia was horror-haven, so for a while they were depicted as THE Black aligned faction. This endured even well after demons returned to the game.
Note that White here is represented by an angel while Black is represented by a horror, presumably phyrexian.
Prior to phyrexian being a creature type, horror was the default type for phyrexian creatures, so unsurprisingly this further enhanced their image as horrorland.
Eventually, horrors would spread to other colors, and eventually so did phyrexia.
Scars of Mirrodin was when New Phyrexia debuted, the glistening oil charged with the mana of all five suns of Mirrodin. This meant a phyrexia now equally divided into five colours. Even then, there was still the overt connection to Black; all colours were given mechanics and effects more in line with Black than how they usually operate, and the default phyrexian token, the germ, was still Black aligned.
From Kaldheim onwards, Phyrexia has been become more “normal” mechanics wise, the only deviation being White having access to poison counters. The redesigned praetors are now not out of place for normal MTG cards of their colours, and the germ was replaced by the colourless mite as the default phyrexian token.
Had phyrexian been designed today, I guarantee a five colour menace would be there since day one. As it stands, we see a slow but meticulous process of lessening Black’s role in the Phyrexian identity, and I hope more non-Black phyrexian cards are to come in March of the Machine.