The same applies in my games. If you create a 2,000gp market price magic item, you only pay 1,000gp to make it, plus the XP, but it still counts against your wealth in full to ensure that you are balanced with everyone else. I run a boatload of different games and I've never seen a problem with this. They only actually "pay" half the cost, as the rules state, but to determine their power level using Table 5-1 in the DMG, it counts against them in full, as the rules state.
The part about that table that a few people seem to find terribly confusing is that they believe the table only applies to treasure "found", which is not the case. The values in that table represent roughly how much wealth they should have due to adventuring. It represents the growth of their pocket books as they increase in level, and the growth of their pocket books is part of what helps you determine how much gear they should have to keep them balanced with the encounters they will face. If they have too much gear, they're too powerful. If they're too powerful, you have to muck with the EL of every encounter to keep them challenged.