I have cleaned up my config file and tried many different things, after literally reading this thread over and all of the unresolved and resolved issues on github. During which managed to learn more about Minecraft and BiomesOPlenty coding. Biometweaker is doing its thing, only that some things done by BoP and Minecraft regarding rivers and other features happens after BT config is applied. BoP keeps applying loamy dirt for Dead Swamps and other biomes, apply dirt with raised rivers/oceans, and apply cluster of dirt along with the ores which some stick out of the surface, regardless of BT modified biome generation.
I am probably going to figure it out the answer with further trial and error...by default the BT config is applied at stage FINISHED_LOAD. If SERVER_STARTING and SERVER_STARTED are valid, can BT commands be applied after the river/ocean hardcode? At least with beaches I can replace them with the wasteland biome while keeping its generation. *goes off to try out this theoretical workaround*
edit: Sigh, nope. Would be great to have a working post-river/ocean/ore gen stage to apply biome tweaks.
edit2: Ah, the dirt only applies to vanilla river. If I use a BoP river and apply the top and filler blocks tweaks, I get want I want while maintaining the river lines. Woot!