I'm trying to understand, what kind of issues might adding all the games in the bundle cause? What kind of "side-effects" could be caused by simply adding the games that I purchased to my library?
I think what they're worried about is people buying, say, https://urocyongames.itch.io/neuraquarium (and I think people should!), then buying the Mega Bundle For Whatever and not being able to find Neuraquarium in their library because it's behind a thousand other things, 99% of which they will never download and aren't really interested in.
The 1% they do will vary according to users' tastes, of course, but I would be very surprised the share of purchasers who download more than a hundred things in a thousand item bundle is more than 10%. (And most of those won't actually play / use what they did do an archive download of.)