When I worked with Clearcase (which is terrible in many ways, this is just one), one of its nice features was that it changed file timestamp to the timestamp of commit, not the timestamp it was changed on developer's machine. The commit timestamp may be after previous commit but also before the compiled object file. Because of this, the only way to do a reliable build was to start from scratch. Which took 45 minutes.
Ceterum censeo, Clearcase must be destroyed.
I don't have a link, but one reason to prefer checksums is if you have intermediary steps that produce artifacts, possibly binary input to another step, that may or may not need to actually be built.
I think in the context of Make it is ok. If you rely on checksums, you must implicitly assume that all commands you execute are idempotent. That assumption easily breaks.