They are to keep you from hyperextending the cast alumium shift forks inside your transmission. Shift fork breakage and damage was a leading killer of the Borg Warner/Tremec T-5's, and I'm sure it's the same with the very similar T-45.
Just keep those stops adjusted properly. One of the biggest reasons everybody recommends aftermarket shifters is to save the tranny from hard part damage.
Pulling away from a stop in 2nd gear isn't too bad. Hopefully you're not running the old 2.73:1 rear gears. The clutch may not like it too much, but as long as you're doing it nicely, you shouldn't encounter a lot of additional wear or glazing. I'd much rather do a $300 hi po clutch than a $1000-1500 tranny.
