AND YET, we are to believe there was no concern that the audience, viewing on black and white televisions of questionable reception, in an episode with someone else commanding Enterprise and Kirk commanding another ship - that just so happened to look like Enterprise - might be a tad confused?
I think that is the point here: considering the odds, fiddling with some tiny decals would neither help nor hinder any.
It's quite a bit more likely that the order of the four available decal digits was chosen at complete random than that any sort of thought went into it.
Why, apart from the single scene where (unambiguously enough) the hero ship first meets the derelict guest ship,
there isn't a scene in "The Doomsday Machine" where you could see the decals! The crucial
Constellation action takes place with the guest ship at a distance, or facing away from the camera. The structuring of the drama conveys the identity of the ship well enough.
And even if an establishing exterior shot of the guest ship might be mistaken for the hero ship for a split second, the action then cuts into the darkened Auxiliary Control where Kirk toils with damaged machinery, dispelling all confusion. And vice versa, no scene aboard the hero ship bears visual or dramaturgical resemblance to those aboard the guest ship.
For the purposes of the plot, the pennants, the names, and indeed the very identities of the two vessels are irrelevant. We only need to know that there are two of them, one with Kirk aboard, the other with the rest. And when the time comes to sacrifice one of the ships, we hear it stated time and again that the guest ship is to perish - but we never quite see this confirmed in a shot of the guest ship's pennants. And we don't need to.
(Admittedly, the person who did the decals need not have thought it through quite that way, as he didn't direct the photography. He might have been thinking in terms of visual confusion vs. terms of continuity, and voting in favor of the former. But the odds are, he was only thinking in terms of "let's make this registry different", without any concern on either visual distinctiveness or continuity.)
Timo Saloniemi