Hi JayG
I used the Transits a few years ago, they are not a bad binding. The laces and lace loops are the week point I found.
The binding should lean forward slightly and this will help give the correct stance. Your back leg should be bent slightly, so this will help with the slight angle. Your front leg should be straighter, and as the boots are angled towards the toes, this should help engage the rail more. When you go toe side, bend both knees slightly more, so that it feels as though your weight is over your knees and the boots are just supporting you.
The transits are a fairly stiff boot, (which I prefer) and this may be why edging feels uncomfortable to you, but they will get more flexible as they age.
The only difference between a wakeboard boot and a kiteboarding boot is the people they are marketed at. I think the transit was actually marked at kiteboarding at some stage.
Hope this helps