If you replace "exist" with other viable conversions like "come upon" or "discover" it makes sense. Even better, a phrase like "described in rigorous detail" helps further to enhance a sense on the writing.
In this situation, depending on context, the writer / orator may be implying
two tones have been come upon, regardless of how many exist
two tones have been discovered thus far, and have been formally dilated as important
two tones have been catalogued as the ones that are exhaustive
Since he's talking about Just tuning, with one tone (the major) having a 9:8 (sesquioctavum), while the minor tone has a 10:9 ratio (sesquinonum), I'm guessing this is an exhaustive list of precisely two things that exist in a theoretic human construction. I think the tuning that Fogliano is talking about is Ptolemy's intense diatonic scale (it could be something similar hwv), a scale that contemporaries like Zarlino revered, and which was mathematically fully elaborated. It's something that exists in nature, but also needed to be "discovered" and systematized/developed by people as a concept.
Moreover, as Lodovico Fogliano clearly pointed out (even if he has taken it from the diatonic tone [system] of Ptolemy) two tones to be established/discovered, the major (9/8) and minor (10/9)..."
Honestly, I have no idea what Benedetti is talking about when he brings up the 65 ratio and 64 rat semitones though. The sesquifourth has something to do with ditone 81/64 ratio. The sesquiquinth is a mystery.
Moreover, as Lodovico Fogliano clearly pointed out (even if he has taken it from the diatonic tone [system] of Ptolemy) two tones to be established/discovered, a major (9/8) and minor (10/9) (that is, a sesquioctave, and a sesquinone) -, and three semitones - a major, a minor [average], and a smallest ["minimum"] (that is, the 65th which is major; the sixty-fourth, that is, the smallest ["minimum"]; and average, as .27 to .25 which proportion is called the proud bipartite twenty-fifth) -, and when he knows that the consonant semitone is the sesquiquinth, the ditone the sesquifourth...[blah blah blah about hexachords]; to the knowledge of all the simple consonances, he put his last hand.