I think that pamphlet got published before the engineering department at Weyerhauser got a chance to look at it.
It's true that MOST of the strength from an I beam (steel or wood) comes from the outermost fibers (which are the 2X3's in this case). However, most of the bending moment in a uniformly loaded beam or one with a point load in the middle is going to be in the middle of the beam. So, it just makes common sense that if you're going to cut big holes in the web of your beams (which will weaken them somewhat), you try to avoid cutting those holes in the middle third of the beam. And, if you're going to cut into your beams, the closer to the ends of the beam you do it, the less you weaken them.
What I'm seeing in that photo is no attempt whatever to move those big holes for the vent closer to the ends of the beams. And, on top of that, there's a great big knot in the wood right under one of those holes. Just because Weyerhauser put their stamp of approval on it, doesn't make it good. I can guarantee you that this brochure is in the public arena because Weyerhauser is counting on the fact that people are going to trust them more than they trust their common sense. What you're seeing there is simply poor planning and poor practice, and those holes should be cut as close the the ends of the beam as possible, and having that hole close to a structural defect in the wood (the big knot) makes me wanna cringe. I wouldn't want that in my house even though Weyerhauser don't see nuffin wrong wid it.
You can strengthen your existing floor joists, and I'd recommend you do that in the area of those big holes. I'd talk to an architectural or structural engineering firm about attaching 1/8 inch thick by 1 and 1/4 inch wide steel strapping to each side of the bottoms of your engineered joists for several feet on either side of those holes. You want to make sure there is no slippage between the wood and the steel, so you'd need to glue the steel to the wood with an adhesive that forms a bond stronger than the wood, and LePage's PL Premium construction adhesive will do that.
If it were me, I would simply buy the steel strapping glue it on to both sides of a joist and then put clamps every few inches to clamp the steel tightly to both sides of the bottom of the joist until the adhesive cures. I don't think you need to use any screws; since they won't matter once the glue cures anyhow.
That way, for the beam to bend when you walk on that floor, the steel strapping has to stretch. Since steel is vastly stronger than wood in tension, attaching the strapping should strengthen the joists considerably, and should make a noticable difference in the way your floor feels.
Since your house is your most valuable asset, you want to do this work with the oversight of an engineering or architectural firm to approve your work.
Or, if that were my house, that's what I'd do.
I think it's stupid to make big holes like that in the webs of the floor joists when there's plenty of room to do it closer to the ends of the joists. Better yet, why didn't they use a better design so that they could just use the space between two joists as the duct itself. I'd prefer even to see a big galvanized duct running under those joists than to see them cut big holes like that in the middle of the joist span.