I have the same shelving unit.
I have a table saw and pretty darn big workshop, but the ease of buying pre-cut 2' X 4' 3/4" plywood panels was just hard to pass up. The pre-cut panels fit perfectly, no trimming at all, and I didn't have lug a full sheet of 3/4" plywood home and cut it up. Just too easy.
I have a 40B on bottom, and 3 20G's on each of two shelves above that. The 20's are all end-view.
The 40B on the bottom has a couple of sections of 2X4 that support the middle of the plywood. There's also a vertical panel in the middle of the second shelf that supports the upper shelf for its' entire 24" depth. So the longest unsupported length is 24".
I wouldn't use 2x4's for all the reasons already given here as well as what you've observed. Also, by the time you add 2X4's and plywood over that, you've added significantly to the height of the horizontal supports and the plywood would most likely not be level on all planes and 1/2" would transmit the irregularities in the 2X4's you've already noticed. Lastly, with all that wood, you may as well make it out of 2X4's from scratch and save the cost of the shelf unit.
"Why can't my wife see all of this stuff as an investment?"