No reason to worry, they are very clear in their position regarding intakes: just as you said, they believe it should be one of the first modifications.
Conveniently, they sell intakes.
IMO the stock intake is very well designed and does its job very well. Any performance gain is not worth using an inadequate filtration system since dirt is a motor's prime enemy after heat. Also, any performance gain is debatable (anybody want to post a statistically significant number of dyno pulls with stock vs. any aftermarket intake?...).