The mod only patches the vanilla files so that seeds are dropped and adds some missing graphics for the seeds.
No seeds are modified, only the kelp files have been patched.
If there are problems then it is either due to incompatibility with other mods or Starbound itself.
I have no interest in Starbound and modding at the moment.
You are welcome to modify the files yourself to make them compatible with another mod.

idk one of the reasons I never used seed maker is that I heard it somehow ended up breaking many different plant mods that I was interested in using

No. You don't get it.
The seed maker does not change the seeds, it merely adds recipes that make them.

Having just this mod won't show any problems since nothing else uses these seeds, but using seed maker reveals the hidden problem.
Whatever this mod is patching is causing a malformation of the base seeds.

the problem must be with the seed maker, because I've had this mod pretty much since it's release in multiple collections and it never gave any problems - and I never used the seed maker

This mod's data may be malformed.
The Seed Maker mod doesn't alter the seeds, it merely adds recipes for them.
When this mod is installed, all seeds are replaced with perfectly generic items.