After looking through the code of Botania and testing, it seems that the way they are registered fails through ProjectE's transmutation system, giving the Botania Flower every time.

Hey, i'm the gravedigger!
Just for other people who have this issue, there is a config file in ProjectE directory : "~/config/ProjectE/nbt_whitelist.cfg" for adding some item who would keep NBT data when transmuted. It seem to be designed especially for this purpose.
nbt_whitelist.zip

That's because the botania flowers have all the same id and metadata, but the various types are defined through NBT.

Just for curiosity: whats the benefit of using NBT instead of having a different metadata value for the different flower types? Botana flowers sound like a perfect example of when to use metadata instead of NBT.

It uses only one block ID. It made more sense in 1.6 but stuck to 1.7.

But using Metadata would also only use 1 block Id. Or was that not possible in 1.6? I don't know.

Using metadata would force me to only 16 different flowers. I'd have to use the name lookup in the TE anyway so what's the point?

Oh right, i forgot, that the metadata is restricted to 16 values for blocks. Items can have a lot more different values though.