About the different “prices”
You seem to be conflating “base price” and “market price”—which is fair, since the rules totally do too.
Every item must have a single—fixed—“base price.” Nothing can change this because it’s an intrinsic property of the item. The rules in the Dungeon Master’s Guide you refer to affect this, because you are talking about different items with different properties, and how those different properties change these separate items’ value relative to one another. (Those rules are also extremely questionable in general, at least if a player is looking at them, but that’s neither here nor there.)
On the other hand, “market price” is, or should be, what NPCs charge PCs to buy the item. (It is also presumably what NPCs charge one another but the rules don’t really care about that.) And the rules state that
For many items, the market price equals the base price.
Because of this statement—and because it’s usually true—the rules are not very careful about using “base price” and “market price” consistently. In fact, I can’t think of a single instance under the rules where they actually differ—the distinction between them exists almost entirely for the sake of DMs who are trying to bring their world to life by making something scarce and valuable, or plentiful and cheap, in particular areas. These kinds of mark-ups or discounts don’t affect the base price. But the rules also never bother themselves to establish any of these, because the rules are very general and don’t get into these kinds of local differences very often. (I’m less familiar with premade modules—it’s entirely possible that Wizards of the Coast did this kind of thing in an official adventure at some point.)
The rules are more careful about the price to craft or create an item, which is usually but not always half the base price. Market price doesn’t come into this, because it’s a question of how hard it is for a PC to create an item with this value—and the single, intrinsic value that every item has is its base price. So, as you note, you have many feats and the like that can change the creation cost of an item—without changing the base price (or, presumably, the market price).
So in short:
Base price is a single, fixed value for each item. If two items have different base prices, they must necessarily be different items, because the difference in base price reflects some difference in their power or “value” as perceived by the author who developed the item. In some sense, the base price is a metagame concept, though it affects in-character values.
Market price is usually the same as base price, and pretty much always the same as the base price in the published rules. The market price is the in-character reflection of the metagame evaluation of the item known as the base price. Any difference between base price and market price is left up to DMs, not codified in rules. (Published adventures may also include some differentiation here as part of the workload they take over for the DM’s convenience.)
Creation costs are a function of base price, another way that metagame evaluation is reflected by in-character realities. Many feats and the like exist to change creation costs, as you note.
Buying low
Comments suggest it is this middle point that you are most interested in: is there anything that says you buy stuff for less than normal?
The answer is yes—but it’s extremely rare, and extremely limited. The thunder guide (Explorer’s Handbook) can gain the ability to buy keiros leaves and covadish leaves at half price in Pylas Talaer, and/or the ability to buy up to 2 healing potions and a Quaal’s feather token at half price in one of the villages on the island of Seren. This is the kind of thing for which market price can diverge from base price.
I could swear there was another prestige class that allowed you to purchase things—anything, apparently—at a small discount (maybe 5%?) in one particular region, probably in Faerûn. I have not been able to find this prestige class as of yet.