The actual river is one chunk east from the river biome, which is not the case when using vanilla world type.

First Image: normal world, same set of mods
Second Image: Lost cities, where the river is one chunk offset to the east.

Modpack: Omnifactory 1.2.2

Minecraft version: 1.12.2

found the problem: in line 26 of the following file:
src/main/java/mcjty/lostcities/dimensions/world/lost/BiomeInfo.java

info.biomesForBiomeCheck = provider.worldObj.getBiomeProvider().getBiomesForGeneration(info.biomesForBiomeCheck, (chunkX - 1) * 4 - 2, chunkZ * 4 - 2, 10, 10);

Not sure why is there a "-1" in (chunkX - 1). My guess is that this feature is intended for generation of buildings, not for terrain.