Although Karel Čapek was raised in a Roman Catholic environment, as he grew older he became intrigued by the philosophical ideas of John Dewey and pragmatism, which are essentially secular, seeing God as a socially useful construct rather than believing literally in the deities of established religions.
In The Last Judgment, God appears as a character who serves as an expert witness and refuses to act as a judge. The anthropomorphic God who appears in the story is obviously not the Christian one in any literal sense, as the Christian God (the Father) is incorporeal.
The notion of God as a witness who does not interfere in the course of human events plays on several rather sophisticated theological concepts. The first is that of the Enlightenment God as a watchmaker who sets the universe in order and establishes the universal laws of nature but does not interfere in the operation of the universe thereafter. Next is a play on a second concept of God as a witness, one appearing in several places in the New Testament, most notably in the Comma Johanneum, and the account of the three heavenly witnesses. Another important reference is the play on Bishop Berkeley's notion that the sound of a tree falling in a forest exists because God is a ubiquitous witness.
In light of these intertextualities, the characterization of God is both apt and clever, albeit as a literary device, not as a literal conceptualization.