I just looked at the design again and realized that there is no fan in the stack, so they probably are using an external fan after the stack, in which case you'd need the duct hole rather than a register grate in order to connect the stack to the fan. I'd still include an airflow deflector inside the stack to smooth the 90 degree transition, and probably a larger duct with final reduction to fan inlet diameter right at the fan. As the design is drawn, there appears to be enough room that you could simply include an inline fan in the stack, which is what I did, placing it at the bottom to keep the center of gravity lower. There's something to be said, though, for using an upflow rather than downflow arrangement, because then you might be able to eliminate a 90 degree bend on the inlet side and the outlet could be straight up through a grate in the top cover, again eliminating a 90 degree bend, plus really big particles could fall to the bottom of the stack without clogging the prefilter.