Sheppy, I don't believe the 3000 ft. height recommendation is just a money spinner, it is there to provide a buffer for serious mishandling of a recovery resulting in a spin.
I am aware of Two events that resulted in spins, one inverted, caused by mishandling during endorsements where the aircraft lost a lot more than 1000 ft.
I know of one 152 student lock up where the aircraft lost 2500ft before the instructor knocked out the student. I've seen 152s and PA28s lose over 1000ft in stalls where the student mishandles the situation. The closer to the ground you are the more likely a student will freeze on the controls when they notice the ground rushing up at them. If you havn't seen this then you do not have a lot of time instructing or you are not really practising stalling.
Don't forget that the closer to the ground you are the more likely the stall may be affected by wind shear or turbulence leading to more likely event of an excursion.
The flying training orgs I've worked for have mostly been trying to cut the cost of training times to be competitive. The minimum 3000ft for stalling was always viewed as a safety margin. It also allows you to let the students stuff up and get to the point you have to recover and show them their error of technique.
If the stalling is conducted as part of basic training you should be revising procedures during the climbs and descent so as not to waste the time.