I don't think I ever found out why pregaps even existed.
CDs were originally intended to have 2 seconds gap between tracks (if you wanted continuous music, then the "index" separation was for that ...) and so all tracks would have a two-seconds "index 0". If you would program a player to play, say, track 3 and then 5 and then 4, it would at the end of track 3 jump to track 1 index 1 (not index 0).
I am not sure what tools will count track 1 index 0 at all if they use the table of contents. But if they do, you use CUETools to create a cuesheet with that pregap.(I caught many more with the AccurateRip ID. dBpoweramp writes those tags, and then CUETools can recognize the CD even without cuesheet.)CUETools may be able to use the AccurateRip ID's in the tags, but I doubt many of the other tools will, like MusicBrainz for instance, and probably most other tagging programs that look up album information based on the album layout (although I haven't actually tried it).