  The Streaming Instability (SI) is a mechanism to concentrate solids in
protoplanetary disks. Nonlinear particle clumping from the SI can trigger
gravitational collapse into planetesimals. To better understand the numerical
robustness of the SI, we perform a suite of vertically-stratified 3D
simulations with fixed physical parameters known to produce strong clumping. We
vary the numerical implementation, namely the computational domain size and the
vertical boundary conditions (vBCs), comparing newly-implemented outflow vBCs
to the previously-used periodic and reflecting vBCs. We find strong particle
clumping by the SI is mostly independent of the vBCs. However, peak particle
densities are higher in larger simulation domains due to a larger particle mass
reservoir. We report SI-triggered zonal flows, i.e., azimuthally-banded radial
variations of gas pressure. These structures have low amplitudes, insufficient
to halt particle radial drift, confirming that particle trapping in gas
pressure maxima is not the mechanism of the SI. We find that outflow vBCs
produce artificially large gas outflow rates at vertical boundaries. However,
the outflow vBCs reduce artificial reflections at vertical boundaries, allowing
more particle sedimentation, and showing less temporal variation and better
convergence with box size. The radial spacing of dense particle filaments is
$\sim0.15$ gas scale heights ($H$) for all vBCs, which sets the feeding zone
for planetesimal growth in self-gravitating simulations. Our results validate
the use of the outflow vBCs in SI simulations, even with vertical boundaries
close ($\leq 0.4H$) to the disk midplane. Overall, our study demonstrates the
numerical robustness of nonlinear particle clumping by the SI.
