I really like the idea of this mod, and was hoping to use it for my current (long-term) save for barreling the water products from Angel's Ores. However, I A) already have a lot of the factory set up to use the canisters and bottles from Bob's mods for certain fluids, and B) have each of these fluids being barreled in one of Bob's pumps/compressors.

I know it's sort of a long shot, but is there any chance of the mod being updated to support either the use of modded pumps or modded containers?

Not really, no. I don't want to add another (mod-specific) set of containers and recipes.

If you want to use this mod as a basis for building your own to package bob's fluids, feel free.