I develop a lot of trees in the ground but don't use colanders or pond baskets. I can get really good root systems just by judicious root pruning. I know there are plenty who swear by baskets in ground but I can't see any advantages.
I would urge you to dig yearly to see how the roots are developing. Digging yearly makes sure no roots get over thick and it is still quite easy to cut through 1 year roots. After 2-3 years roots of some species can get thick and hard which makes digging a real chore. Regular root pruning also helps the roots ramify into lots of small feeder roots closer to the trunk which is needed for life in a small bonsai pot.
Pomegranate and citrus are often a bit slower so may benefit from 2 years at a time but be prepared to change depending on how they appear to be growing.
Trees will grow in soil but, depending what the soil is like, may do better with some additives to break up dense clays or really rocky soils. My native soils are quite good so I just add some compost and manures to help open the structure a bit. There should be no problem changing the roots to bonsai type mixes when they go into pots.
3-5 years is not overly optimistic to develop trunks in ground but be prepared for a few more years after that to grow the branches and final leaders in pots before finally calling them bonsai.