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When a bonsai is referred to have been grafted, context, I’ve just watched a YouTube video and the narrator stated showing the bottom of the stem / trunk, “ you can see where it was grafted” showing a clear difference between the earth level trunk and the tree trunk above.

Does this mean somehow a separate tree was grown on the original trunk of another ?

Lee.

Yes, grafting is the process of fusing two different plant materials onto each others. Sometimes it is tw different species and sometimes it is branch from the same species or even the same tree.

I’ve seen a few videos now where a grafting line is visible where the trunk comes out of the substrate almost as if two separate trees were fused together at this point! Is that a thing? If so, how do you get them to stick together?

Yes, it is a "thing". There are many different techniques for grafting depending on what one wants to achieve.

In bonsai grafted trunks is generally considered a bad feature. Trees on its own roots is allways better designvice.

Grafting is often used to improve foliage on juniper; for example ;Juniperus parsonii with Juniperus itoigawa, so you have the best on both worlds.
This is next level techniques, I never tried it so specialized advice is wanted before you start.

I do believe that the most common graft In bonsai is japanese white pine on japanese black pine roots. It does not always look very good, but the benefit is much less sensitive to root rot and much faster development.

The most common grafts oitside the bonsai world is edible apple trees. All apple trees with sweet tasting fruits are grafted.