Rusty_Gunn: it helps with modding, while the CS can point to an item in a BSA file, I don't think it can browse through BSA's.
Expanding on both, the historic and practical reasons, for the loose files outside of Steam.
How BSA (Bethesda Softworks Archive) files work, they are special archives used to package game files by Bethesda, this is true now but, maybe not the original disc release for Morrowind.
Every mod can also use these, but traditionally that was rare and for the older games, modders would unpack all Vanilla files, and the original disc releases of old (GOG's sources, are not Steam's repacks), may have come with loose files for Morrowind, maybe even Oblivion, but modders would never usually use the BSA packages, as Loose files always override any within BSA's.
Regardless of what the CS can do, user made tools have always existed, to unpack and pack all BSA's, but the disc of Morrowind predates Steam, and loose was favoured for modded and vanilla files.
When the Steam Workshop arrived, suddenly it demanded all mods came with only two files.
An ESP (Plugin) and a BSA, even a simple texture replacer must do this, even though it needs no plugin.
With a 256 file limit for plugins, including all the Vanilla DLC, having a plugin for a simple texture swap makes no sense.
Then we have the advanced modders who through merging techniques can have 500 or more Plugins, in their modded game, and a hundred thousand, or more loose files.
Many mods only contain the loose files, and need no plugins at all, but the 256 limit always must be adhered to.
So reducing the Plugin count is always better for mods.
With Skyrim came a New Mod Manager (Mod Organizer) that allows mods to use BSA's, yet treat the contents as loose files anyway. A best of Both worlds setup, the SSD saving smaller size archives provide, and the user control of loose files.
But Steam/Bethesda now disapprove of loose files (After Workshop), they had other ideas on who should control mods, as many like me predicted, from the day the workshop appeared.
The workshop was always intended to dominate and destroy the Nexus and other sites.
Only the fact, it was so bad, a mere downloader, pretending to manage mods, needing the Vanilla Launcher, for any actual management, basic as that is, without it the single "Subscribe" button, is nothing but download.
Think about that, Steam Workshop is a glorified download manager, created for Skyrim. Yet from day 1 you "Subscribed" to Workshop mods, instead of downloading them.
Subscription infers payment, preconditioning the mass acceptance, which failed, but the intent is now, and was always clear.
When instead of 95% of modders flocking to Steam (A major concern at the time), they fled to Nexus instead.
The Workshop made modding much more popular, but most of those new recruits, used NexusMods, within hours of starting.
The original paid mods scheme was delayed, then with Fallout 4 imminent, they sacrificed Skyrim Mods, on the altar of the Gods of More Mooney than Sense. Thinking they got paid for that already, it can take the flack now, then Fallout 4 mods can be sold from day 1.
The Fallout was much worse than they expected, but neither Valve or Bethesda have given up on it.
Just to be clear there's nothing wrong with paying Mod authors for mods, if it's a new franchise where that's clear from before anything is sold, but sell the game, with the understanding, that mods can never be sold, and this is written in the EULA , wot unchangeable legally, but it's morally set in stone, and as was made clear totally unacceptable, whatever the law allows.
The key definition of a mod is based on control and selection of content.
Modding can be restricted, as the Skyrim Workshop shows, these are mods, but restricted mods.
The line is crossed if selection isn't 100% under the mod users control, selection can't be restricted, only the user must choose what mods they will and won't use, from all available mods.
What makes a mod available, uploading and releasing to the public, where is not a factor, anywhere where it's available to all with the game, on the platform(s), it's made for.
When a Publisher or even worse, Retail Store (Online Client), selects what content is available, and more importantly isn't allowed to exist, that content is by definition Publisher provided DLC.
It can never be mods, under those conditions, regardless of price.
If the penny hasn't dropped, I'll spell it out, Valve's flagship games, DOTA2 TF2 and CSGO, have no mods at all, everything available is Valve DLC.
The potential is clear, if Bethesda Softworks, selects the so called "Console Mods", they will be Bethesda DLC on consoles, but still mods on PC, which is strange, but that's what it would be, I must make clear, I don't expect this to happen, Bethesda appears to understand this, they vetoed Valve Selection for Skyrim, at start of Workshop and again for paid mods, and Valve still don't understand why.
Though dev tools are great, if modding relied on them, it wouldn't exist.
Modding relies on total user control of all the content, if it's on your PC, you have total control.
The other thing modding relies on is that, what can be coded by one developer and/or team, can be hacked and changed by another developer and/or team.
Modders are just developers, and many are much better, than the ones paid to make the game.
I guarantee, modding devs know more about the Creation Engine, than the entire staff at Bethesda Game Studios.
The day that Fallout 4 released, we had a better set of Ini files, Vanilla, is full of long obsolete settings.
All that was needed, was to actually test them in game, BGS never even tried.