For solid bodies that share a face and need to be "glued" together, there are ways to achieve that connection that is neither bonded contact nor fixed joint. You can use "Shared Topology" and have the elements on each side of the coincident faces share nodes. The benefit of this is a smaller model. You can get the same effect with Node Merge if each face has mesh controls to force the nodes to line up. Shared topology does this automatically.
Imagine two tubes that are placed end-to-end and the annular faces need to be connected. Bonded contact puts elements between individual nodes over the whole face and creates a very localized connection. Say the other end of one tube is a fixed support and the far end of the other tube has a lateral load so the tube is a cantilevered beam and some bending occurs. In the annular ring, the force is transmitted locally all around the face. Depending on the contact formulation, you can get some penetration of nodes into the target surface. That doesn't happen with the shared topology method.
A fixed joint creates a point at the centroid of the faces, and builds a spider of elements out to all the nodes on each face. All the forces and moments go through that one point. That is one of the benefits of using a joint, you can easily extract those quantities from your model. But there is no local node-to-node forces transferred around the annular face. The force has to go down the spider, though the point and back out on another spider to get to the other side.
There is a danger when creating joints in Mechanical. Never use duplicate on a joint in the Outline to make another joint to use elsewhere in the model because the point that was created for the first joint is used in the new joint, rather that being updated to the location of the new faces. That means the invisible spiders that are created can go from one of the new faces, all the way over to a point on the other side of your model through a point, and then all the way back. You can imagine that a small tension on the tubes of the new joint will have a result that includes a HUGE moment, and a small force, when it should have a zero moment. This can cause the solver to have convergence difficulties. This kind of mistake cannot happen with bonded contact.
When there is a significant gap between the faces that need to be "glued together", the fixed joint will always work by simply choosing the two faces, but bonded contact may not create any contact elements and the bodies will not be glued. The corrective action is to type in a Pinball radius to make sure that the contact elements are created. You should always insert the Contact Tool and Generate Initial Contact Status before you start the Solver. You don't need to to that for Fixed Joints.