3000 feet was where Insight network became operational, and Zola's Algorithm started picking out threats to hydra, that naturally would include everything in LOS that could launch a counter attack on the Insights. iirc, the charts showed the Insights continuing their ascent up into sub-orbit, and sub-orbital capacity was mentioned. And of course there's no other way that just three helicarriers could globally project instant force, unless they're sub-orbital death-from-the-skies.

Also, in plot terms, 3000 feet is around where it's still believable that people could be having a fight on the un-pressurised deck tops.