It's interesting that upon initiating barter with Knight Torres, she says,

"Our patrols are always picking up new things,"

Seeing as there are no patrols given McNamara's lockdown protocols!

-RRR: So, Bethesda, how do you explain this incongruity?
-B: Oops! Our bad! I salute RRR's keen intellect on our mistake though! Here's a 12.7mm bullet on us. Put it through the head of a super mutant for us!

Honestly though, lets play the apologist game and try to rationalize what these "patrols" are and how Knight Torres is getting supplies, not to mention why she'd sell anything at all. It's not like the Brotherhood deal in the uncouth tender of *raises nose snobbishly* bottle caps *condescending, British, parlor laugh* aha... aha... aha...

Do Brotherhood members even need to buy things from quartermasters? They're a communal technotheocracy, not the Marine Corps. Even if some chapters did force their members to pay for supplies, I doubt the supplies in question would stretch beyond energy weapons, power cells, hydraulic fluid, and spare servos.

For some chapters, it makes sense, such as Lyons' Brotherhood, which its condition of ultimate heresy *gasp* lets outsiders join. With these kinds of uneducated conscripts, it would probably be necessary to stock a bunch of non-energy weapons and low-tech armor.

Err... I believe McNamara DOES say that despite the lockdown being active, there are still patrols out there. Also confirmed by Mr. New Vegas' news show saying something like: "Shady figures spotted around Hidden Valley."

The lockdown obviously isn't complete. There are patrols at night in the hidden valley. Also, there are some scouts, and of course the 3 dead BoS who were sent to look for supplies.

McNamara sends out special runners to fetch specified supplies, Veronica being one of them. He does not send out patrols of paladins and knights for combat missions and technology recovery, as a normal chapter would do. The hulking figures described by Mr. New Vegas are Brotherhood members going through security rounds that don't stretch beyond Hidden Valley. The only other cases where Brotherhood members left the bunker to find tech was the three groups that the Courier finds all dead.

This does appear to be true. Although the runners like Veronica might explain the Brotherhood's need for wasteland currency, as they might use it to buy essential supplies, like food, from wastelanders. That still doesn't adress where the things they sell are coming from though, it also seems like a somewhat flimsy justification, seeing as it's not exactly common practice to let random wastelanders into the bunker and trade with them, in fact the Courier appears to be the first person to be granted such treatment by the Mojave chapter, thus meaning they could not acquire bottle caps in this means before the Courier came along, yet they obviously had a source of these supplies before that.

I'd say it's because Obsidian wanted to put a trader in Hidden Valley and hadn't really clearly thought through how to make it make sense, but what you're asking for is an explanation for it that DOES make sense, so that isn't really satisfactory.

Though you made a little mistake on your own part in your opening post, since New Vegas is developed by Obsidian, not Bethesda, so I'd imagine that if you want an explanation for anything that doesn't make immediate sense, they ones you should be asking are probably Obsidian.

As a military outpost a quartermaster is essential, as seen by the laser pistol event.
As posted by Selbeth, caps will be needed for general trade with outsiders ( which the BoS always has done ).
That and some times I think Veronica references gifts, which I assume a BoS member would be able to barter for or are deemed non standard issue.
So would be charged for by the QM if in stock as a way to both regulate supplies and provide stress relief to members.
EW's, PA and rations among other high tech pieces would be signed out and monitered, everything else would be up for grabs imo.

Tht's all the lore reasons, in game it's just a way to make sure you get another well stocked supplier with some good equipment at mid - late levels.
It's a pity you don't get supplies free when your rep gets high enough with factions ( I know there's "gifts" like ammo for some stimpacks / food for others ).
As I know game "balance" is what matters, but not everyone of my characters loots everything, and finds it silly to do so given certain roles.

Torres does not run "shop", she is quartermaster. She just happen to trade with player. Same as NCR quartermaster in F. Hope for example. As for caps, they always comes in handy when trading with outside, like Veronica does. And given BOS doesn't have currency of their own, they may use caps themselves. As BOS members do have private property, there is no reason why would they then not trade it between each other or even their quartermaster.

Supplies may come from older stocks, trade with outsiders, local manufacture. There is even workshop inside bunker. And there are still some patrols out there, its not like lockdown is absolute.

I really see nothing strange in it.

Don't blame Bethesda for Obsidians writing slip ups. :spotted owl:

This isn't a writing goof. If you stand outside the Hidden Valley bunker at 2am, you can actually see a patrol on its way out. Elder McNamara even explains that the artificial dust storms at night are there specifically to mask the comings and goings of their occasional patrols. The lockdown is just there to prevent the average Brotherhood members from leaving (but it's not even airtight for this, considering examples like the two initiates who sneak out with Torres's Missing Laser Pistol).

Where does it say that members of the Brotherhood have to pay for these supplies? Aren't you told that even though you have been given permission to get supplies you have to pay for them? I believe you're told the same thing by the NCR Quartermaster at Camp Mojave.

I found nothing in the game to indicate that any faction charges their own members. Did I miss something?

Well. If you use Fallout:Tactics as a source, BoS recruits get almost nothing and are expected to forage for new equipment, and trade in what they find to their base QM.

Or if you adopt a more sane viewpoint, BoS members probably get some equipment issued to them. And it's probably completely baseline, beat-up, pre-used-fifty-times-over equipment that gets the job done and nothing more. So if there is an option to buy something better for their own personal use, they'd probably be interested. Though given how old this stuff is, it's less "buy new equipment" and more "buy maintenance work from the workshop". This is the same phenomenon that you see with real life hunters and their constant cleaning and accessorizing even though a hundred year old rifle that was lost in a gravel pit for most of its lifetime will kill a target just as dead as your brand new, 80% plastic, oddly chambered rifle.