This lets me grow cells with one of the click substrates, say, a methionine substitute that incorporates into every protein, purify out my protein, and then easily do chemistry on that. That's near invaluable.
I can grow a virus and put a different click substrate in each of the DNA, protein, and lipids. Then I can infect cells, and mid-infection, separately label each macromolecule a different color. Then, I can figure out what parts of the virus go into the cell, which sheds light on the mechanism of entry.
Having it bio-orthogonal means the biology is preserved and nothing is messed up until the moment of observation.