The report discusses leaving spacers in place as a possible source of discoloration. The leveling systems clips are designed to break off at the base, essentially the bottom of the tile. Good prep prior to grouting should remove any bits, if there were any, and make this a non-issue. The only situation where it is more likely to happen would be with maybe a glass tile, or a VERY thin one, and those aren't good candidates for those leveling systems for the most part, partly because they tend to be small, and partly because they may be transparent or translucent, so ANYTHING under them would show, especially poor technique with the mortar, and almost certainly what was left of any leveling clip.
Some grout color unevenness goes away after things fully cure, too, but could be an issue for the first day or two. Similar to some porous stones becoming discolored by the moisture from the thinset...depending on the situation, it can take a couple of weeks for it to return to 'normal'.