Cooperative Crafting increases the value of what you are crafting per day, not the amount of things being crafted in any given time, nor the amount of time you take to create a potion/scroll. Valet familiars gain the feat even if they do not meet the requirements.
If your crafting limit was 1,000 per day, with a valet familiar, this limit is now 2,000 per day. But what the feat helps with is the Crafting Progress you make each day. If you would take 10 days to craft a 10,000 gp magic sword, with a valet familiar helping you, this task now takes 5 days.
For potions and scrolls, that are normally 250 gp per 2-hours work, it doesn't become 500 gp per 2-hours, but means that your daily progress will be limited at 2,000 gp. Which makes the feat only useful for higher level scrolls or potions crafted using a higher level caster level, as potions are capped at 3rd level.
You cannot craft two items at once, nor you can craft twice the amount of potions. You are still limited by other rules:
Potions and scrolls take 2 hours per 250 gp on their price, or 1 day per 2,000 gp on their price.
Other magic items take 1 day per 2,000 gp on their price.
The GM could house-rule that it also increases the 2-hour limit for potions and scrolls, but that's not what says on the feat.
For 3.5e, there are a couple of different ways (Especially since you say a bit of cheese, for that I am going to borrow a little from other systems/homebrew).
From the Eberron Campaign Setting (Pages 52, 53 and 56) there are three feats, Exceptional (Reduces time), Extraordinary (reduces cost) and Legendary (reduces XP) Artisan, the texts are as follows:
EXCEPTIONAL ARTISAN
[ITEM CREATION]
You are an expert at creating magic items faster than usual
Prerequisites: Any item creation feat.
Benefit: When determining the time you need to craft any item, reduce the base time by 25%
EXTRAORDINARY ARTISAN
[ITEM CREATION]
You are an expert at creating magic items at a lower cost than usual.
Prerequisite: Any item creation feat.
Benefit: When determining the gold piece cost in raw materials you
need to craft any item, reduce the base price by 25%
LEGENDARY ARTISAN
[ITEM CREATION]
You have mastered the method of creating magic items.
Prerequisite: Any item creation feat.
Benefit: When determining your XP cost for creating any magic item,
reduce the base cost by 25%
That's what I found from official sources. Now for some of the cheese, including borrowing from other rulesets and a homebrew item.
If you borrow from Pathfinder, there is a general feat called Cooperative Crafting, which allows you to speed up crafting with the help of an assistant:
Cooperative Crafting Your assistance makes item crafting far more efficient.
Prerequisites: 1 rank in any Craft skill, any item creation feat.
Benefit: You can assist another character in crafting mundane and
magical items. You must both possess the relevant Craft skill or item
creation feat, but either one of you can fulfill any other
prerequisites for crafting the item. You provide a +2 circumstance
bonus on any Craft or Spellcraft checks related to making an item, and
your assistance doubles the gp value of items that can be crafted each
day.
I did also run across a homebrew item, Fast Item Creation, which adds to the GP value that can be created in a day, reduces the time, and stacks with itself (No opinion given on how much it can break things):
Fast Item Creation [Magical] Spellcasters can create items faster.
Prerequisite: Ability to cast 4th level spells
Benefit: You increase the daily rate at which you create magical items by 1000 gp.
Normal: All spellcasters normally create items at the rate of 1000 gp per day.
Special: This feat can be taken several times, and stacks with itself.
Each time it is chosen, add 1000 gp to the value of a single magical item that the character can create per day. Thus, items take half the usual time to create with one feat's worth of Fast Item Creation, one-third the usual time with two, and so on. A minimum of one day is still required for the creation of any item, however. In campaigns using Psionics this feat can also be used to speed up the creation of psionic items, for those that meet an alternative (or additional) prerequisite of the ability to manifest 4th level powers.
Best Answer
This depends entirely on what it means to make an item “with” a particular item-creation feat. Extraordinary Artisan is classed as an item-creation feat, so you can choose it with Magical Artisan, and it’s a fair reading of Magical Artisan to say that “normal” here means “as it would be without this feat,” so when you make an item “with” Extraordinary Artisan, the benefit of Extraordinary and Magical Artisan would stack.1
The real question is, do you ever make an item “with” Extraordinary Artisan, and as I said, that comes down entirely what “with” means here. There is no external commentary on this feat or what that usage of “with” is intended to mean. It could mean that we are only talking about the feat that is required to make the item, or it could mean any item-creation feat involved in the process, which Extraordinary Artisan would be. This can really go either way.
That said, Magical Artisan is a feat from a Faerûn supplement, while Extraordinary Artisan is from an Eberron supplement. Magical Artisan was also published about three months before Extraordinary Artisan was, and it’s entirely possible that the Faerûn team had limited interaction with and awareness of the work going into the new Eberron campaign setting. Furthermore, as you point out, choosing Extraordinary Artisan effectively eliminates the entire point of picking an item-creation feat, since you could then go on to choose Extraordinary Artisan for every item you ever make. That seems very unlikely to have been an intended combination; if the authors intended that, they should have just eliminated the choice altogether.2
So while I think that from a rules-as-written perspective, you can make a case for Extraordinary Artisan working here (and wouldn’t bat an eye at it being used so in a theoretical-optimization exercise), I think there’s vanishingly little justification for expecting such a ruling in a real game. If a DM actually wants to allow it, he or she would be better off houseruling Magical Artisan to not be limited to a single feat in the first place.
Note that if you have both Extraordinary Artisan and Magical Artisan choosing some other item-creation feat, you would absolutely benefit from both when using the chosen item-creation feat. This answer focuses specifically on the choice of Extraordinary Artisan, but I felt it important to note that there are ways to combine the two regardless of how one decides the issue of choosing Extraordinary Artisan itself.
Monte Cook, of course, did make claims that Wizards of the Coast occasionally did intentionally put clearly-superior options into the game to reward system mastery. Personally, I consider that kind of dubious in general, and certainly don’t see any evidence that this is what took place here.