Critical break in is 1,000 miles.
Other things may happen over the next 10-20K miles, but who is to say that it won't break in properly after a chip is put in the car (and what exactly are those "other things" anyway)? The transmission probably takes a good 20K miles to break in.
The only reason you shouldn't chip for the first 1K miles is that you'll be compelled to step on it! Personally, based on Audi's guidelines about engine break in, I wouldn't have any problem chipping after 1K.
Chipped since birth (well, 2K)...