Meantone tuning, or just intonation. Its rich flavour derives from pure thirds (the mean or middle) & fifths in major white note scales, but the 'price' for this is that the black note scales are unusable.
Werckmeister, a late 17thC modification of meantone, is designed to retain some extra 'flavour' in the white note scales, while facilitating passing use of black note scales.
Equal temperament. Here all the notes are equally spaced allowing modulation between all keys. The drawback is that it sounds bland because no thirds & fifths are perfectly in tune.
Every harpsichordist spends a considerable time tuning. It's a strangely private world as you listen to the musical intervals forming and reflect how much variety in the fine tuning is actually possible within the relatively narrow parameters which the harmonics allow. The 'devil' in tuning arises from a natural anomaly identified by Pythagoras, that a cycle of ascending perfectly tuned fifths (C0-C7) reaches a higher pitch than seven straight octaves. This acoustic anomaly is known as the syntonic or Pythagorean comma.
Given that 'intunity' makes such a difference to musical enjoyment for performers and listeners alike, it's strange that the subject is considered too arcane for public discussion. Western ears have become so lazily accustomed to the equal-tempered major scale that any alternative tuning strikes most people as weird. But in terms of musical history equal-temperament is of recent history. Like the history of timbre in Western music there is a symbiotic relationship between temperament (tuning) & chromaticism (use of notes outside the seven note scale).
What is interesting about this particular piece is that it was written in this epoch, c1600, that composers were first beginning to expand their tonal range beyond the diatonic (staying within the seven note scale) and to explore the additional range of tonal and emotional colours which chromatic notes make possible. Fantasia Chromatica is doubly interesting because altho it's technically demanding the music is written within a 3.5 octave compass making it playable on the average virginals or organ of the period.
At that stage the technical evolution of keyboard instruments was not far out of its infancy. Apart from its chromaticism the Fantasia Chromatica is firmly within the modal traditions of church polyphony, and shows little influence of the dance-inspired music being written for public entertainment in England and Italy.
In the style of modal music which evolved within an ecclesiastical context what was wanted was a continuum of sound. Therefore modulations (key changes) were kept to a minimum, and even adventurous composers like Byrd or Bull do not explore dramatic contrasts of key - as opposed to dramatic effects within a tonal range. One of the reasons for this was that people tuned keyboard instruments in just intonation in order to maximise the harmonic richness of the white note keys, and saw no occasion to venture outside them.
If you listen to a typical set of folk song variations by William Byrd from around this time you hear that the diatonic character of the melody makes no demands on its harmonic environment. In fact the whole piece uses only white note keys, and as such it is possible to maximise the richness of its effect by tuning the major white note scales 'perfectly' since the black note scales are not required. At that stage 'art music' remained strongly linked to the voice, and thus the parameters of vocal melody prescribed all musical thinking, and thus the idea of experiments with dramatic modulation are rarely found except, ironically, in some early Italian madrigals.
Given the way in which keyboard instrument technology evolved in its early stages, restriction to white note keys was inevitable. This painting of an organ by Van Eyck from 1432 shows that keys were of extremely short depth, rendering all but simple music impossible. I myself have played the 1612 Ruckers virginals in Fenton House, London; and can confirm that the key depth is so short that a modern keyboard techniq with substantical use of the thumb is all but impossible.
As composers experimented with increasing harmonic complexity in the 17thC many theorists experimented with modifying the existing temperament more or less radically. One whose proposed temperament of 1691 strikes a happy medium is Andreas Werckmeister, which I have adopted as a halfway house.
But even this did not satisfy the next generation, and it was Bach who pioneered the cause of equal temperament by writing the first of two sets of Preludes and Fugues in every maor and minor key in 1722 his Wöhltemperierte Klavier (Equal-Temperament Keyboard). From that point onward the idea of modulation took hold of composers' imagination, notably Bach's son Carl, from which the whole 'technology' of classical ere key antithesis derives.