Just have found, that the bug has place only if "Consider mesh UVs" flag is set. When un-set and re-bake combined material, texture area in atlas become proportional to source import size. There are no multiple maps, because it is simplest "Mobile/Unlit+Lightmap" shader. Also, while experimenting with atlas size, when I set it to 32768, script crashed with OOM on Texture2D constructor, and it is not a problem, but it changed import settings for all source textures to uncompressed with read/write enabled. So I have to manually restore import settings. Maybe it is worth to wrap baker with try-finally block?