Q:

How to calculate the proper layer height multiples?

We all know, that the best layer hight is, when you have multiples of full steps. If it is not, sometimes steps get skipped and end up bad layer-to-layer adhesion when one height step missed a tiny bit and then the next catches up, creating an extra-thick layer. For example, this was printed somewhat deliberately, and here, the extra spaced layers are perfect for delaminating the print with just a fingernail:

The Ender 3 I have uses the following Z-Rod:

Diameter 8 mm
4 flutes
ca 13 Threads per inch

That is according to the table, a 2 mm pitch for one thread.
As a result, it's an 8 mm pitch for each of the 4 threads.

The firmware (Marlin) I use claims in configuration.h that the NEMA17 motor would be using 400 Steps per mm in Z. configuration_adv.h tells that the microsteps on the Z-axis motor are 16.
In the printer's menu, Babystepping is in increments of 0.049 mm (though some rounding error seems to be there: 5 Babysteps are 0.250 mm).

A:

that the NEMA17 motor would be using 400 Steps per mm in Z. configuration_adv.h tells that the microsteps on the Z-axis motor are 16.

Easy. There are 400 microsteps in a millimeter, and 16 microsteps in a full step. So, there are 400/16=25 full steps in a millimeter. So a full step is 1/25th of a millimeter, or 0.04 mm. Your layer height should be a multiple of this.
As your leadscrew has a lead of 8 mm (i.e., a full rotation will move the Z-axis by 8 mm), a full step is either 8/200=0.04 mm (for a 1.8 degree stepper) or 8/400=0.02 mm (for a 0.9 degree stepper). So, apparently, you have a 1.8 degree stepper (and this is the most common type of stepper).

