Try and cram 800 objects (actually, almost 900, since most vanilla bigobs are in use as well) in 999 slots while retaining any space whatsoever for doing it orderly. Even if I did, at a price of insanity while trying to link corpses to their respectible bigobs (which is a price no one in their right mind would pay), there's only a slight stretch from 900 to 1000. Probably already broken by the extra 150 corpse items added by Ivan's mod; and if not, sure to be broken before 1.0 release.
Floorobs do not nearly approach the limits since doing them properly is a big slowdown, but space must be reserved none the less for eventual inclusion of dozens, if not hundreds of floorobs where now only stand-ins are used.
As for the handobs, the limit is actually 125, (since each is occupying 8 spaces), so my 200 already is well over that.
In each of these cases, going over 1000 (but not using huge numbers like 100000) resulted in wrong files getting attributed, or the game outright crashing.
Having said that, I'm interested in your explanations.
PS. Also while your solution is true for normal mods, "master mods" are more severely constrained. Several solutions were proposed when the system was being implemented, but Warboy's defence of 'one 1000-size fits all' was absolute.