Enemies packs and zoning...

1) Lobos everywhere! they almost fill half of the whole packs list and covers all the zones of Veldt... which Lobos are actually used/necessary for the game? i'd like to replace all that useless packs with new formations and monsters;

As far as I've noticed, only the first 1x Lobo formation is used. It's an event battle in Narshe and a monster in a box in the beginner's house.

2) Like lobos, i believe there's some other formation not labeled as dummied content in the game which still won't show... for example in zoning(above 127) there are too much leafers... any knowledge to share?

I think those are zones for town or dungeon areas that have no encounters. Why a leafer was used instead of a lobo, I don't know (EDIT: It's because Pack 0 has leafers in it). Zones are stored in the same order as the location maps, which is how a zone gets assigned to a location.

3) In the Packs screen there's a mysterious flag for all 4 formation slots which says: "Rand. w/next 3"... what does it mean and how it works?

This is used only for the Floating Continent. Because the map is so large, the developers wanted to have more than 4 possible formations to encounter. So, they created this flag that increases it from 4 to 16 possible formations... you'll notice that the next 3 packs are all Floating Continent encounters too, so it chooses randomly between those four packs. I haven't tried using the flag outside of the Floating Continent though.

4) Zoning: first 128(0 to 127) slots are used for battles in WoB and WoR... How 'bout the other 128? some slot is clearly used for dungeons and bosses?(so the note says) but not all the slots... how they work?
And even more important: how grass/forest/dry land and desert slots affects the ones after 127? and finally how can you use unused slots of zoning?

As I mentioned before, the last 128 zones are dungeon and town zones, and are stored in the same order as the maps themselves (there is no lookup table). The grass/forest/dry land slots are not based on terrain in dungeons or towns. What you are really seeing, are four zones for four different maps. It's not about terrain at all. The interface is kind of misleading in that way.