I'm not sure to what extent this is fixable or gamebreaking (probably not much), but biomes that would be one type in 1.2.4 continue generating as a different type in 1.3.0. For example, one biome that was to be a savannah continues as a magical forest.

Not fixable. When BYG has updates to its biome generation (or any mod adding/removing biomes) then it remakes the biome map, aka which biomes are placed where. This causes biome chunk borders.