Well.. could you perhaps change your mod info to something like this?
"dependencies": ["base >= 0.15", "? boblogistics >= 0.0.0"]
because in my specific setup, it ended up making bob's underground belts non-replaceable with the base ones...
So I figured the reason must have been that bob's is loaded after Fast Replace Underground Belt.
Though, it's likely preferable to find a way to load this mod last in every case to have maximum 3rd-party belt compatibility... but the load order might be hard to predict without optional dependencies...
Edit: well.. or maybe just use data-final-fixes.lua because that also worked for me and does what's needed, execute those data changes last.
http://lua-api.factorio.com/latest/Data-Lifecycle.html