It may be that the seeds available at embark are hardcoded, then.
It cannot possibly be hardcoded, since the plants are all defined in the raws (and can be removed and replaced with other ones).
The underlying assumption you're making isn't true.
In the Accelerated module of the Modest Mod I replaced all woods (except Nether-cap) with generic wood. When you go to prepare carefully for embark, the game spits out errors about not being able to find their woods by their default names. (Also, IIRC, apple wood for some reason.) So, the fact that a given material is defined in the raws, doesn't mean that it isn't hardcoded as part of embark logic.
The mod is linked in my sig if you want to verify.
But were these errors due to the game or due to the embark profile? The latter uses specific material names but is not technically hardcoded.
Embark profiles also irritatingly refer to your embark party by position number with no chance to re-order them... but that's a completely unrelated rant that I totally don't bring up at every opportunity...
Happens even without using an embark profile. I very rarely use embark profiles - pretty much only when I've generated a world specifically for plant testing.