The way pre-loads work exactly is that the depots as they existed upon a game becoming pre-loadable (Steam's backend keeps older versions of depots, which is why
even Valve can roll back patches when necessary) are downloaded in an encrypted state, provided of course they're included in your package. The reason there is often a relatively small download period upon unlock is that the data no longer matches, so Steam has to download what is essentially a patch -- there are no missing files, aside from perhaps the executable in cases where the game in question is using CEG ("Steam DRM"), due to
how it works.
But, yeah, you're absolutely right that there's no justification for a lack of a proper pre-load period. Even if Konami spent a few days fiddling with the data and it resulted in a 5GB "patch" on release day, that'd be preferable to downloading the whole hog for just about everybody.