The former is basically within a big enough city you can buy most wondrous items without a ton of effort.
The latter is a certain number of magic items are available in a city depending on rarity with occasional influx of new items.
To me it seems like a question between convenience and immersion. Thoughts?
PF is high magic, so having a local magic-mart is a thing. Other systems had less magic, and so they were not.
Even with magic-marts, getting custom stuff is still hard, and commissioning it takes forever due to a production rate of one day per thousand gp. [Costs extra to get faster.]
I have no problem with magic-marts, but don't use them much even when there. I want too much custom stuff. With the crafting rules in place, it is relatively easy to craft custom stuff.
I think the immersion problem you see is actually a poorly described environment. The Myth Adventures series of books describe bazaars with lots of magic that don't break immersion.
The convenience problem is usually tied to a lack of roleplay in locating the vendor and the store (expensive stuff) or stall (cheap stuff) that sells the items. Sometimes, the vendor is only a broker that knows who is selling what, and for a fee, they will arrange a trade. If the players don't take the time to play this, it looses immersion, and becomes convenience.
/cevah
In a city or metropolis there are usually enough wealthy patrons to make very high end specialty stores economically viable (i.e., the really high-end jewelry stores, car dealerships, fashion clothiers, etc.; you find them in NYC, LA, London, etc., not in your local mall).
However, it is unlikely that you will find one vendor that will sell every type of item (or even every type of wondrous item)*; which is what it seems that those who are against the "magic mart" imply (or outright state without justification) 3.x/Pathfinder requires. As Cevah states, this is probably because the GM hand-waves the selling/purchasing of magic items to get back to the "important" adventure/campaign plotline, instead of "wasting time" on the PCs' changing/upgrading their equipment.
Then again, playing out the PCs' "downtime" activities can often increase the players' sense of immersion: by presenting the appearance of a "living, breathing world," instead of one that barely exists "outside of the dungeon/needs of the plot" (which was a common complaint, even in 1st Ed AD&D).
*- You could easily have one vendor selling just magic bows and arrows, a different one only selling magic melee weapons, a third with nothing except armor, etc.
I tend to find the default PF Settlement rules work pretty well, to be honest- there's a gold limit on general items that can be found without much effort, and then a handful of more expensive magical items exist in the city at any given time. The result is, if you're adventuring in small villages that don't have access to many magical items, you naturally won't be everything you want. The "magic mart" basically is extremely limited at that level, limited to scrolls and first level wands, mostly. On the other hand, if the players are lucky enough to have access to a metropolis, they have a "magic mart" effect, at least until the upper levels. Thankfully, the GM has control over the cities they place in their world, and therefore can choose the extent to which they have magic items be available. (If you're running a premade adventure though, then magic item availability is going to be part of the texture of that adventure, if you choose to use the magic item rules)
The big takeaway here for me is that settlement size has a profound impact on the flavor of the players adventures, if you use the normal rules. Think about what settlements you want to them to start the story with access to, what the upper limit of settlements should be in your adventure, and what the players will do once they pass that upper limit, and you should have a fairly natural magic item availability progression.