Lokiyn, you seem to be missing a few crucial things.
First, the magic item creation rules do not actually mention allowing you to use metamagic modified spells in an item's creation. Any attempts to do so place your work in homebrew territory. Also, the standard rule for homebrewing items with spells modified by metamagic is that the level of the spell slot is what would be used to calculate an item's cost, not its effective level. The price for a wand of Empowered Burning Hands would use 3rd for the spell level, and minimum 5 for the CL (if a wizard makes it, 6 for a sorc, etc). It would still have an effective spell level of 1st things such as dispelling or protecting against it, or save DC.
Second, Sanctum Spell does not change the ACTUAL level of the spell, only its EFFECTIVE level. This means that while it will lower the item's save DC while used outside your sanctum, or raise it when within that area, it does not change the spell slot required, and therefore will not change the item's creation cost. Remember, item creation cost is not an effect of the spell, and therefore is not subject to a spell's effective level.
Third, whoever supplies the spell(s) to be used in the item creation must be able to CAST said spell(s), meaning they must still meet the minimum ability score required to cast them. If an item is used, it automatically uses the minimum required ability score (10+spell level). This is reinforced by the concept that a 1st level warmage cannot contribute his Fireball to the creation of an item, because he is too low in level to cast it, even though he knows all spells on his list. Or if his charisma is below 13, for that matter.