Well, the OHMSS one is the only one that ever appeared in any release versions. It was quickly recalled and replaced with the Thunderball credit. It is unknown how many prints were released with OHMSS listed or if it was only the premiere engagements.

IMDB is not an accurate source to use as it is frequently full of user posts that merely repeat urban legends etc. No version I know of ever had 003 seconds shown as it was Harry Saltzman who insisted they need to go back during editing a replace it with the insert of the counter reading 007. It was so late in the game there was no time to adjust Bond’s line about the three more ticks.

I have never heard of the blip of Bond and Pussy escaping the plane being missing. The shot and music cue is timed to show that blip of escape at exactly the last second. The only difference I might expect is in the end credits akin to Thunderball where some versions might have Barry’s ending music instead of the title song. (TB has Barry’s Mr. Kiss Kiss Bang Bang in a custom instrumental in the regular mono and in the remix with alternate dialogue there is the JB theme slapped on.) Of course this is merely me speculating as I think they had early on decided to drop Barry’s end cue for a reprise of the title song.