Anual plants die each year, it is the definition for anual plants! The seeds are another different individual, and the parent plant is dead.
The pupa metaphore I think that is incorrect and missleading, a pupa is a stage of a living individual that is also metabolically very very active, and is an instair to get to adult form. If you want to make a metaphore for anual plants maybe the best one is a dead mother spider (or other animal) with their eggs close to it; so you could focus your observation on the mother or the eggs, that are two clearly different individuals.
If the observation is made for the paternal dead plant then the answer is that the plant is dead. Marking dead anual plants could be very helpful for climatic and ecological research; answering questions like when the anual plants start to die each year, and how this compare to past years. Also some anual plants individuals might die without a chance to make seeds before dying.
If you make an observation showing seeds that seam to be alive, then you might say that the plant is alive, but then could be useful to add a “seed” or “seed stage” annotation or something like that.
I get that this could be confusing for some geophytes, because they look like there are dead in some seasons, but the individuals are still alive underground, and also there are some other questions like when an anual plant might be consider dead, so not sure if the value that we might get from the alive-dead annotation would be worth the complex determination.