The Dungeon Master's Guide offers the following:
Armor for Unusual Creatures: The cost of armor for nonhumanoid creatures, as well as for creatures who are neither Small nor Medium, varies from the values given on Tables 7–3 and 7–4, as described in the Armor for Unusual Creatures sidebar on page 123 of the Player’s Handbook. The cost of the masterwork quality and any magical enhancement remains the same. (DMG p.217)
Thus, only the cost entry in the table for armor is affected by that rule; that is - only the mundane, non-masterwork price of the armor is affected.
For the example of +1 full plate armor made for a large creature, the cost would be 4,150 GP. 3,000 GP from doubling the cost of medium full plate armor, 1,000 GP from the +1 enhancement, and 150 GP from the masterwork armor component. [Do note that armor enhancement costs and weapon enhancement costs are not the same. Your question seems to assume that a +1 armor enhancement costs 2,000 GP, which it does not.]