You can find examples of both color schemes, and others, throughout history. It all depends on what was popular at the time and what a customer wanted to order.
Early on, in Europe, the "natural" keys were made of ebony or ebony veneer, while the "accidental keys" were of plain maple.
Later on, it became possible and affordable to import elephant ivory from Africa, and to construct ivory veneer to laminate to wooden keys. Somebody got the idea to make the accidental keys of ebony to contrast with the ivory on the natural keys.
It is entirely a manner of style of course. It has nothing to do with playing the instrument.
Some keyboard instruments were plain in their appearance, while others were very fancy and used expensive decorative woods and wood veneers, as well as elaborate painting and artwork.
At all times in history, as with today, you could order an instrument that was as plain or as elaborate as you were willing to pay for.
A Ruckers harpsichord from the mid-1600s with custom-made deluxe ornamentation
A contemporary replica of a Ruckers model from the mid-1600s without all the ornamentation, and with white natural keys and black accidental keys