The report leaves out a crucial detail; the total number of STEM degrees increased significantly. Doing some backwards math, the total number of STEM degrees increased by 108% (x2.08) between 1988 to 2016. The US population only increased ~35% in the same period. Even if we assume the increase in the college age population was a bit higher (accounting for birth rate decline), the overall trend is growth in STEM degrees by both native and foreign students.

Given how much population and economic growth the main sources of foreign exchange students had during the same period, what we see is expected unless we actively tried to limit foreign exchange students. Native students aren't being replaced, they are still there.

We don't depend on visas to 'sustain' our economy. We use immigration to keep the massive comparative advantage we have had for the last ~80 years (since WW2). It's classic brain drain and the US has been on the winning side for most of recent history.