This was a change made as a result of feedback. Originally the seeds were taken at the start of the process - but this meant that if something happens such as an extended region crash or the person has to take their bed back into inventory for any reason the seeds are lost along with the item being grown - this led to a request to move the ingredient to be taken at the end of the process. Monitoring your seed usage may be a little frustrating but losing them altogether is far more so.