I believe the etch factor is something the PCB manufacturer has to worry about, not the PCB designer. The etch factor is just the amount of 'oversize' the manufacturer has to add to get the right trace width when it's done etching. The effect on the actual trace only limits the minimum width. Referring to your reference document, the minimum trace width difference between 1 oz and 3 oz copper is only .002" (.007" vs .005"); that's not much, especially considering that the OP intends to have large currents and, thus, large trace widths; otherwise, why would he be using 3 oz to begin with? In other words, if the OP needs a .005" trace, why is he using 3 oz copper?