In fact, Fux was basically a reference text on 16th-c. counterpoint in its most complex and developed form, as it was understood after-the-fact in a 18th-c. context. It doesn't do much to pedagogically explain even the simpler foundations of 16th-c. style (as they show up in earlier texts), let alone tonal counterpoint in the common practice period.
> common harmonic sequences
Common harmonic sequences are not voice-leading schemata. If anything, the former are a side-effect of the latter. Even teaching cadences as a "harmonic" motion rather than a pattern involving the melodic motions of tenorizans (2^--1^) cantizans (8^--7^--8^) and bassizans (5^--1^) is a very flawed understanding that would've been quite foreign to 18th-c. musicians.
As for the thoroughbass, the older textbooks may give a cursory explanation of the notation involved, but what about the practice of it? Where is the règle de l'octave - the "harmonic" bread-and-butter of so much music of the common practice, known even to amateur accompanists back in the 18th c.? A lot of the time, it isn't there. And that's literally the simplest and most basic part, there's plenty of more involved patterns that musicians back then would've known in some way.
Again, I am confused by your claims. The species system taught by Fux is, as far as I recall, the exact same way that counterpoint is introduced in, e.g., Gauldin's "A Practical Approach to 18th Century Counterpoint." (Gauldin goes into much more detail on other things, but the approaches are consistent.)
The fact that the upper voice goes 2-1 or 7-1 and the bass 5-1 at cadences is one of the first things taught in a counterpoint class. The rule of the octave is in most theory textbooks. The first example that comes to mind is Laitz, "The Complete Musician."
You're right that these textbooks don't teach how to improvise an accompaniment from a figured bass, but I'm not sure that's a good use of time for a theory class.
> common harmonic sequences
Common harmonic sequences are not voice-leading schemata. If anything, the former are a side-effect of the latter. Even teaching cadences as a "harmonic" motion rather than a pattern involving the melodic motions of tenorizans (2^--1^) cantizans (8^--7^--8^) and bassizans (5^--1^) is a very flawed understanding that would've been quite foreign to 18th-c. musicians.
As for the thoroughbass, the older textbooks may give a cursory explanation of the notation involved, but what about the practice of it? Where is the règle de l'octave - the "harmonic" bread-and-butter of so much music of the common practice, known even to amateur accompanists back in the 18th c.? A lot of the time, it isn't there. And that's literally the simplest and most basic part, there's plenty of more involved patterns that musicians back then would've known in some way.