It's genetics - certain varieties of Ficus (usually ginseng) grow fat caudexes naturally. It's not something you 'do' or not. There are very many types of Ficus and recently ginseng has been sold all over - just the latest fad! Ficus benjamina, for instance, will never grow bulbous trunks like that, or ones out of proportion to the top of the trunk, even if they gradually become much thicker all around over time.

Do moreton bay figs grow fat caudexes naturally when grown from seed?

No, but may grow lots of aerial roots like the retusas do.

Is there any way to encourage moreton bays to grow interesting aerial roots when they are quite young. I have a namaqua rock fig (ficus cordata) that has a fat base and looks a bit similar to the retusa, but it has thicker and flatter leaves.

Lots of humidity is the key, and if you get some starters, guide them into drinking straws stuck into the soil, pack moss around where they grow from the trunk/branches, and keep it moist (not soggy) and wait til they grow into the soil. If you can get those straws with bends in them (like hospitals use), it would probably look more natural for ones growing from the trunk (not as rigid).

Thanks Lucy.