Botania version
r1.9-340

Modpack
All The Mods: Expert v1.0.24

See screenshot:

Ahh weird. I do have optifine installed. Is optifine what moves flowers around randomly from their grid position or is botania doing that?

I think, maybe both. Don't have time to do any testing right now, but maybe Optifine and Botania are using different random seeds (?)

I think this is mostly a bug on Optifine's side. Botania flowers extend BlockFlower just as they should and don't appear to be doing any other shifting.

the hitbox not matching the visual shift is a vanilla bug fixed in 1.11

Vanilla is the one that does the small random shift in any flower position.
I can't tell if this bigger shift is related with Optifine or not, can't reproduce.

I think this only happens with Optifine.