The Digikey article appears to be talking about digital inputs. Your application is analog.
SS14 is a Schottky diode which is leaky, particularly at high temperatures. 10mA at rated voltage maximum at 100°C and 200uA at 25°C. A leakage of 0.5mA will cause an error of more than 1V. Probably it won't be that much at room temperature and 3.3V reverse voltage, but it will likely be measurable.
More seriously, a 0.5W 3.9V Zener diode will also conduct significantly at 3.3V. Here is data for the 500mW MELF diode series including 3.9V MLL5228A. Vz for the MLL5228A is specified at 20mA, so it appears to be the 4th curve from the left. At 3V it will typically conduct around 1.5mA. Some zeners are specified at much lower Vz and they will conduct less (at both 3.3V and at 3.9V).
So that circuit will affect the accuracy considerably and the effect will vary considerably with temperature.
Designing clamps that work without adding excessive error to precision analog signals is not altogether straightforward, and the first step is to determine your required accuracy and what maximum level of input voltage you are trying to protect against.
You will also need to know what maximum input impedance the STM32 MCU can tolerate without undue ill effects. And how much current you are willing to allow the STM32 input protection networks to conduct.
Eg: Re comment, here is the general idea. It's also possible to use the emitter of a PNP BJT to clamp the voltage, provided there's a bit of current draw guaranteed from the 3.3V supply. Base to 3.3V, collector to ground.
simulate this circuit – Schematic created using CircuitLab