Multiple codes are available to derive atmospheric parameters and individual chemical abundances from high-resolution spectra of AFGKM stars. Almost every spectroscopist has its own preferences regarding which code and method to use. But intrinsic differences between codes and methods lead to complex systematics that depend on multiple variables such as the selected spectral regions and the radiative transfer code used. I expanded iSpec, the popular open source spectroscopic tool, to support the most known radiative transfer codes and I assessed their similarities and biases when using multiple setups based on the equivalent width method and the synthetic spectral fitting technique (interpolating from a pre-computed grid of spectra or synthesizing with interpolated model atmospheres). This work shows that systematics on atmospheric parameter and abundances between most of the codes can be reduced when using the same method and a careful spectral feature selection is executed, but it may not be possible to ignore the remaining differences depending on what is the scientific case and the required precision. Regarding methods, equivalent width-based and spectrum fitting-analyses exhibit large differences that emerge due to their intrinsic differences, which is relevant given the popularity of these two methods. The results help us identify the key caveats of modern spectroscopy that any scientist should be aware of before trusting its own results or being tempted to combine atmospheric parameters and abundances from the literature.