I'd like to request a config option that disables the lowered ocean floor level.
Main reason is Railcraft: Railcraft generates geodes in oceans. With the lowered floor level you loose more than half of the resources generated by these geodes.
Buildcraft oil springs also don't look too shiny with those very deep oceans.

The lowered ocean floor is only in the Oceanic Abyss ocean biome, which is already configurable in the biomegen config file.

That is not the case in my worlds. Did another check today with only the following mods:

Minecraft 1.6.4
Forge 953
BoP build 359
CodeChickenCore 0.9.0.6
NEI 1.6.1.5
MobiusCore 1.0.4
Opis 1.1.0
CodeChickenLib 1.0.0.36
WorldCore 1.1.0.17

Results are like in the attached screenshot. Normal ocean biome (not abyss) is significantley deeper than for example kelp forest or coral reef (aprox y-level 30). Both the later are like vanilla oceans. Abyss is even deeper.

Ah, my bad, turns out that this only occurs in the vanilla ocean biome as we don't override it. So, as a result of our height changes, it becomes a lot deeper. We'll take a look at this in 1.7 since they would've likely changed it while they were adding 256 height support.