Signals don't have to make it across the whole die each clock pulse. They just have to make it to the next register in their pipeline/data path, and timing tools for that absolutely exist. They treat it as analog because the signals themselves are analog and chips must account for things like the time it takes for a signal to go from a 0 to a 1 (or vice versa), as well as the time it takes to "charge" a flip flop so that it registers the signal change and holds it stable for the next stage of the pipeline.