Assuming all three match, you know that the binary matches the source.
Someone who is more technically inclined can probably go into more detail on this.
For the curious: we actually were intentional about finding these, by compiling many programs with the same parameters on different machines. One with a 32 bit OS and toolchain, the other one on a 64 bit machine, and we would get alerted when we produced binaries with a different checksum.