yeah but if you do plan on getting the GT4 engine, it will make mince meat of a manual 5S-FE box. I believe the 3S-GE box is much stronger (not 100% on this thou).
I guess it depends on what you finally want to achieve. If you really want the GT4, get the proper 3S-GE box. If you are keeping the 5S-FE SX motor, then of course the standard manual gearbox will be fine.