Let's run through an example: Say someone where to introduce a new model for the Leviathan to replace the one currently in 3.8.2
The 3.8.2 model has several destroyable armor plates modeled onto the ship - in leviathan.pof - which are disabled by mv_assets_t-shp.tbm, which also calls for the game to use Leviathan.pof instead of cruiser01.pof as per retail ships.tbl:
$Name: GTC Leviathan
+nocreate
$POF File: leviathan.pof
[irrelevant data cut for time]
$Subsystem: armour01a, 1, 0.0
$Flags: ( "collide submodel" "untargetable" )
$Subsystem: armour02a, 1, 0.0
$Flags: ( "collide submodel" "untargetable" )
$Subsystem: armour03a, 1, 0.0
$Flags: ( "collide submodel" "untargetable" )
$Subsystem: armour04a, 1, 0.0
$Flags: ( "collide submodel" "untargetable" )
$Subsystem: armour05a, 1, 0.0
$Flags: ( "collide submodel" "untargetable" )
$Subsystem: armour06a, 1, 0.0
$Flags: ( "collide submodel" "untargetable" )
$Subsystem: armour07a, 1, 0.0
$Flags: ( "collide submodel" "untargetable" )
Now if you were to replace with Leviathan.pof in the package is going to be mv_assets_t.vp you only ever have to edit the files that go into that package, and without having to edit anything else. So if you were going to use for-argument-levi.pof instead of Leviathan.pof you would have just to change mv_assets_t-shp.tbm to exchange the referrence under $pof file: and remove all referrences to the now no longer existing subsystems armour01a through armor07a which would no longer exist in the hypothetical for-argument-levi.pof. No other package would have to be touched.
These steps are no that different if you were to consolidate all MVPs into a single package or consolidate the tables in one place; with one big exception - keeping track of all edits and coordination them with multiple contributors.
As the MVPs are structured now you could easily assign each package an individual version number, so you can track which edits occur when. With the packages individually versioned, you can track which changes have been made and also more easily roll back a change that doesn't work out, as any change would just be contained to a single package.
Of course, none of that you would see on the user end - which makes it extra arcane looking - but helps to organize a work process.