Kalki seems to just kill almost every human, with the notable exception of Devapi and Maru. The Mahabharata seems to skirt around this issue, understandably given its controversial nature, but you can tell that's what it really means. It is said in multiple places that the literal definition of a varna is based upon
character/behavior, although it is inheritable to a debatable extent. The references to the Chaturvarna there can easily be explained by the other races such as Asuras.
And Markandeya said,
...
And the whole world will be filled with mleccha behaviour and notions and ceremonies, and sacrifices will cease and joy will be nowhere and general rejoicing will disappear. And men will rob the possession of helpless persons of those that are friendless and of wisdoms also. And, possessed of small energy and strength, without knowledge and given to avarice and folly and sinful practices men will accept with joy the gifts made by wicked people with words of contempt.
...
And Brahmanas and Kshatriyas and Vaisyas will disappear, leaving, O king, no remnants of their orders. And all men towards the end of the Yuga will become members of one common order, without distinction of any kind. And sires will not forgive sons, and sons will not forgive sires. And when the end approaches, wives will not wait upon and serve their husbands. And at such a time men will seek those countries where wheat and barley form the staple food.
And, O monarch, both men and women will become perfectly free in their behaviour and will not tolerate one another’s acts. And, O Yudhishthira, the whole world will be mlecchified. And men will cease to gratify the gods by offerings of Sraddhas. And no one will listen to the words of others and no one will be regarded as a preceptor by another.
...
And no one will, at that time, be a giver (of wealth or anything else) in respect to any one else. And the inhabited regions of the earth will be afflicted with dearth and famine, and the highways will be filled with lustful men and women of evil repute. And, at such a time, the women will also entertain an aversion towards their husbands. And without doubt all men will adopt the behaviour of the mlecchas, become omnivorous without distinction, and cruel in all their acts, when the end of the Yuga will come.
...
And he will restore order and peace in this world crowded with creatures and contradictory in its course. And that blazing Brahmana of mighty intellect, having appeared, will destroy all things. And he will be the Destroyer of all, and will inaugurate a new Yuga. And surrounded by the Brahmanas, that Brahmana will exterminate all the mlecchas wherever those low and despicable persons may take refuge."
So Kalki will kill the Buddhists, but it is completely unrelated to them being Buddhists. He just kills every human minus Devapi and Maru (possibly others, but I see no reason to believe so), so kills them for the same reason as all the other humans.
Don't worry though, Kalki leaves the structures intact. Thus, all our hard work will help a new, better race of humans flourish.
And in the age that will set in, viz., the Krita, well-planted gardens and sacrificial compounds and large tanks and educational centres for the cultivation of Brahmanic lore and ponds and temples will re-appear everywhere. And the ceremonies and rites of sacrifices will also begin to be performed. And the Brahmanas will become good and honest, and the regenerate ones, devoted to ascetic austerities, will become Munis and the asylums of ascetics, which had before been filled with wretches will once more be homes of men devoted to truth, and men in general will begin to honour and practise truth.
https://www.wisdomlib.org/hinduism/book/the-mahabharata-mohan/d/doc7469.html#note-e-28433