The even weirder part is that they wanted to hold on to "Walk On" and "Elevation" for later...as if they were worried that their future work would be so weak that it would require those songs to help out the compilation. Hell, one of the band members even mentioned this in an interview with Interference years back if you care to dig it up (pre-HTDAAB, I believe). Like, either go all-in and include all the key tracks from ATYCLB or just keep the collection focused on the 90s.
The other really dumb thing about including "Beautiful Day" and "Stuck" is that practically anybody interested in U2 at the time had already purchased a copy of All That You Can't Leave Behind, so it's not like they really helped boost the sales of that compilation whatsoever. Might have even dampened it in some people's eyes as the casual audience might have been more inclined to purchase a release with even less material that they didn't previously own. And long term, the inclusion of those two songs wasn't much of a boost because they went and cannibalized the sales of The Best Ofs by introducing U218Singles into the marketplace.
I think it was actually dumber to have two tracks from 2002 included on the compilation. And then to have those, but not include "The Ground Beneath Her Feet" or "Walk On" or "Elevation" makes it all really confusing...and then they 00s-ed a bunch of 90s songs with those Mike Hedges mixes...
And aside from ignoring Pop on future tours, the U2 that would come after that compilation's release would be much more willing to embrace the 90s. The Fly becomes a regular concert staple while the 360 Tour ends up finishing with a huge chunk of Achtung Baby. Meanwhile, a bunch of Zooropa/Passengers tracks make live appearance, many becoming tour staples.
The Best of 1990-2000 was basically released when U2 was at their most scared to be adventurous, although ironically, when they were probably still not too concerned about having a hit. Now they're willing to be plenty adventurous, but then want to trim off the rough edges in order to have hits, giving us material that satisfies very few. Say what you will about All That You Can't Leave Behind, but it's easily their most organic release of the century. A pop record from four guys who could give a fuck. But then its overwhelming success blinded everything.