Unfortunately I'm running into this situation where blossom berry seeds have missing transparency when planted. This occurs for every growth stage of the crop. I'll update this if I find other seeds that do this (this is the first one so far).

Forgot to add my example photo:

Update: This ONLY occurs with the blossom berry.

As it turns out, there is also an issue with the Umbrella Tree (however, this only happens inside a Botany Pot... though none of the other saplings have this issue...):

Which version of the mod are you using? This should have been fixed in 1.4.1

Ah, I'm on 1.4.0. The problem is that GDLauncher doesn't display the updates to me because I guess this isn't marked as compatible with 1.16.5.

I haven't moved to 1.16.5 officially yet, but you should be able to play fine with 1.4.1. Update ;-) and..before you report it, the umbrella tree sapling transparency has not been fixed in 1.4.1 yet though, because there seems to be a problem with the texture itself. The other blocks i had just forgot to set as cutout..woops