Scientific transliteration of Cyrillic into Latin was first introduced in 1898 as part of the standardization process for the Preußische Instruktionen (PI) in 1899.
The deviations are with щ, where the transliteration makes clear that two phonemes are involved, and џ, where it fails to represent the (monophonemic) affricate with a single letter.
The transliteration system is based on the Gaj's Latin alphabet used in Serbo-Croatian, in which each letter corresponds directly to a Cyrillic letter in Bosnian, Montenegrin and Serbian official standards, and was heavily based on the earlier Czech alphabet.
The Cyrillic letter х, representing the sound [x] as in Bach, was romanized h in Serbo-Croatian, but in German-speaking countries the native digraph ch was used instead.
[1] It was codified in the 1898 Prussian Instructions for libraries, or Preußische Instruktionen (PI), which were adopted in Central Europe and Scandinavia.