Is the transformer's secondary winding too large?
If you're going to use a MOT as a 'normal' transformer, then be aware it's been optimised to the max for low cost and high power output, when blown with a fan. This results in the flux and consequently the magnetising current being very high, comparable with the load current. It's good to put another 25 primary turns on (50 outside the US) to reduce the target volts/turn and hence magnetising current.

It's really difficult to reclose a MOT core and get good small airgaps in the iron path. Excessive airgaps will mean yet higher magnetisation current. If you're winding a low voltage transformer, then the best method when you salvage your next MOT is to leave the core intact, and cut off the HV winding with a saw. Having knocked out the shunts, wind the new secondary by threading plastic-insulated wire through the core, it's only a few turns. Add as many of the extra 25 primary turns as you can be bothered to by the same method.

To answer your question, as long as the wire passes through the hole in the iron, it doesn't matter where in the iron window it is. Excess length of the turn won't affect the off-load voltage, but the extra resistance will cause a lower on-load voltage because of IR volt drop.