@chrislandy the problem with locking your feet in on any water ski or wakeboard is eventually you are going to over stress ligaments or bones and they break! Absolutely you do not want one foot in and one out, that leads to disaster! The older you get the easier it is to break something for most people. And if you have ever had a serious injury, requiring surgery, you will want to find a way to avoid it again.
Given that you are building your own trick ski, you can easily put inserts in place to accommodate your boots. However as @eleeski pointed out, performance may not be optimal. Especially as you shift weigh forward and back. But you can use a rubber wakeboard boot without the heel for the back toe plate.