I think there are a few issues here
1.) Rarity is based on effect, not duration. A potion of fly and a carpet of flying both allow flight; which the game views as being very rare. Sure, the potion is a one-and-done, but the fact is if you need to fly, it doesn't matter HOW you do it, what matters is that you have an item that lets you do something impossible for no "cost".
2.) Rarity means more for the world than the PC. A +1 sword doesn't change how the world works; its uncommon because it really is only a step up from a regular blade (which still works, even if its an inferior good). A carpet of flying has no mundane equivalent; PCs fly via magic or they don't. A world where potions of flying are uncommon means people would have a reasonable* chance of finding one; which would mean more people have the ability to fly than expected.
3.) Potions are really measured by their own thing (as are scrolls), permanent items are another. Its not fair to compare them, even if they are the same rarity.
4.) Cost per rarity is a guideline; considering crafting is optional (as is buying/selling), their is no real reason to map out items to the last GP (and in 15 years of d20, its proven to be a fool's errand anyway) the costs are guidelines, and it seems lots of people are already modifying them to suit their own magic item distribution tastes. What the table does is provide a start point: does a +1 sword cost hundreds, thousands, or ten-thousand's of gold to make?
5.) Really, all rarity means is "this item is more powerful than a similar item one rarity level below it." Items don't map to one another in terms of power, nor does it mean that they are interchangable (4e tried that with magic items. Yawn). It basically a "hey, watch before you give a low level PC a staff of power". warning.
The system works fine in terms of goal-posts (a few oddities nonwithstanding) but trying to turn it into a system akin to 3e/4e is a lesson in disappointment.