Borders are absolutely in the star Trek utopia. Everything has borders. What we do about those borders is the difference.

Each quadrant, solar system, etc has borders. These are even more arbitrary as the current state, county, and country borders across our world tend to follow natural terrain or longitude and latitude. None of these exist in space. But the quadrant borders are as easy to cross as for me to drive to my next US state. However, the Kardassian border is not so easy to cross, just like it’s not so easy for me to cross into North Korea.

Borders are not the inherent issue here. Conflict is the inherent issue, and borders are how we try to minimize that conflict.