I'm not sure what they mean by after market transmission. No one else makes MB transmissions. It might be that they put in a transmission that was not the transmission that was in your car and that was rebuilt by another shop. As long as they're comfortable with it and stand by the warranty, you shouldn't have any problems.
What I would do is compare the transmission number in the unit you now have with your original unit. The part number and transmission model for your car should be something like 126-270-46-01 722.310. If what's in your car now reads differently, it was originally off another type of MB. It's a common practice among rebuilders. I don't know how acceptable it is.
FWIW, when I got my 81 SD, it had a 722.309 transmission (280E) tweaked to work in my car. I've since replaced it with a 722.315 transmission (300Dt) also tweaked to work in my car. I have no idea who does all this tweaking.