> ridership is down from its peak
Because Metro's reputation suffered when operations couldn't keep up with rising ridership. What will prevent Metro's operations from suffering again when an influx of Amazon employees stresses the system again? Would it be better if those workers got onto the already-jammed freeways?
> against the prevailing flow
Only if they board the trains between the downtown core and Crystal City. Odds are, if they're boarding from the northwest or from newly gentrified neighborhoods, they need to pass through the downtown core to get to Crystal City, which puts them on the same trains as people commuting in from the suburbs. They may get on pretty close to where the suburban commuters get off, but there's still an overlap. Not to mention the overcrowding on the downtown core platforms themselves. Keep in mind as well that Crystal City-bound trains from the downtown core stop at the Pentagon first, which has its own non-negligible share of commuters - those trains may not be full, but they sure aren't empty.