OK Oldschool. I'll lay down some more of what I think I know about magnets. But bear in mind, I am a lowly mechanical engineer, have not been exposed to electronic stuff and it is only interesting to me. The only reason I have even a passing familiarity with the subject is that I collect antique engines and the magnetos are usually the hardest item to get working properly. Have tools and facilities to re-charge many of them.
A flywheel magneto typically has the magnet cast into the flywheel. The flywheel is then machined [typically] and the magnet remagnetized. These manufacturing considerations somewhat limit the types and shapes of magnets that can logically be utilized.
The voltage generated in the coils of the wire in the 'pick-up' coil, and across the condenser, is not only determined by the flux density [the magnetic strength] but also on how fast the magnet moves past the core ends [the laminated iron core of the coil that is close to the flywheel]. Therefore at higher rpm, where the mixture is more difficult to fire, the magneto blessedly provides a hotter spark. Just like God [and Mr.Briggs and Mr. Stratten] meant for it to do. So the search for, and even the belief that it would be an improvement, in the rpm range that counts, is largely unwarranted [in flywheel systems where the magnet moves past the coil rather than than in a design such as a 'armature' moving past a stationary magnet as in the Hunt or Morris magneto on your Harley drag bike].
The most commonly used magnet for magneto application is the cast Alnico 5. They are fairly easy to manufacture and shape all the way up to an 8 field strength. It is possible some folks are providing the better numbered Alnico magnets but I would not bet on it. The more common commercial magnets are Alnico and Ceramic. Also, Neodymium, and Samarium types ; these two are the rare earth magnets. Alnico magnets are named after their main constituents; aluminum, nickel and cobalt. They have the widest range of temperature stability of any standard magnetic material. [Engines get hot and would ruin some other types]. Alnico magnets like to have lengths that are long in comparison to their cross sectional dimensions. [[A perfect attribute for a magnet that has to be as long as the coil's laminated core and the rim of the flywheel as thin as possible [to lessen the chance of flywheel explosion] for a flywheel magneto application]].
Ceramic magnets; so called because of the molded powder blanks are then 'sintered' at about 2000 degrees F. similar to kilning of pottery. Mostly made of strontium carbonate and iron oxide. They have really good magnetic strength but they are also have a bad problem that to my knowledge has not been worked out. They have inherent imperfections; cracks, porosity, voids, surface finish problems and etc. so they have not been used, to my knowledge, in a flywheel magneto system. They are simply not structurally reliable enough for any but a demented engineer to consider their use.
More on rare earth magnets. They are called "rare earth" magnets because neodymium and sumarium are classified as such in the Periodic Table. These guys have 5 or more times the energy of Alnico magnets. Again, they are magnetized through their thickness rather than their length. Neodymium rare earth magnets will rust. Cannot be subjected to temperatures exceeding approx. 180 degrees F. The Sumarium type rare earth magnet is most expensive [more expensive that an expensive magnet] but eliminates the rust problem and is a better choice for use in elevated temperatures but are not as magnetically strong as the Neodymium type.
Both types of rare earth magnets should not be ground or machined on as it produces a dust that is a fire or explosion risk.
With little exception all magnet materials are "oriented"at some point in the manufacturing process. This means that they can only be magnetized through one specific direction. Conventional magnification is straight through the orientation direction and, of course, produces a North and a South pole. The rare earth magnets are extremely difficult to magnetize in the conventional way, i.e, with the North and South poles at opposite ends of the long axis. So a rare earth magnet would need to be [not only as long as the coil's laminated core ends] but radically very thick. That fact leaves the engineer and the manufacturers with the option of not using a rare earth or a flywheel with a much thicker rim. And providing, in most all cases, an over-kill design and last but not least a more expensive and less reliable system.
If you say that some after-market flywheels are equiped with neo magnets I'll have to believe you. But I'm having trouble believing it is a good idea unless there has been some significant gains in technology. To the best of my knowledge there would only be a gain in the mind of the person that spent the extra bucks.