<p>I have a Prusa MK2.5 which runs at 12 V, the Prusa MK3 runs at 24 V.</p>
<p>I noticed that on <a href="https://www.prusa3d.com/product/stepper-motors-set/" rel="nofollow noreferrer">Prusa's webpage</a>, they list the stepper motors as being compatible with both the MK2 <em>and</em> the MK3 even though they run at different voltages.</p>
<p>My question is: are stepper motors typically tuned for specific voltages (like most fans are), or are these stepper motors compatible with <em>both</em> 12 and 24 V systems?</p>

Without having the exact model number of the motor to check the data sheet, this can't be answered.  Glancing at the link you supplied, I didn't see either a data sheet or a model number I could use to get a data sheet.
Typically stepper motors overheat when they are run at too high of a voltage.  However, the advertised voltage for the motor could be the lowest voltage at which it works.
For a real answer, you'd have to look at the manufacturer's datasheet for the motor, which should include minimum and maximum voltages and graphs showing current vs. voltage vs. force graphs, and possibly duty cycle graphs.
Also, in some cases, if you run a motor at a higher voltage than it is rated for, it may produce back EMF that is larger than the motor controller is prepared for, and it could burn out the controller.  However, if the controller is designed for 24v, this is less likely of a problem.
Note also that there are conversion kits, where you place a small board between the controller and the motor that fixes the voltage for the motor.