Buoyancy Confusion- What does the weighing scale show when a block is at the bottom of the beaker? What does the weighing scale show when a block is at the bottom of the beaker?
Is it equal to the weight of the beaker plus the weight of the mass? The issue I have with this is when a other scenarios such as mass floating the upthrust plus weight of beaker is shown on the scale, however here the upthrust is less than the weight?
 A: 
The issue I have with this is when a other scenarios such as mass
  floating the upthrust plus weight of beaker is shown on the scale,
  however here the upthrust is less than the weight?

Under any of these scenarios, the scale will show the sum of the weight of the beaker and the weight of the block. The upthrust could be viewed as an internal force in the beaker-block system, which should have no effect on the interaction of the system with the scale.
If you still want to understand the internal forces in the scenario, when the block is at the bottom of the beaker, you have to take into account the normal force, acting on the beaker in addition to the upthrust due to the buoyant force. In the static equilibrium, the sum of these two forces is equal to the weight of the block and, therefore, according to the Newton's third law, the force of the block on the beaker is equal to its weight.
This is equivalent to adding the weight of the block to the weight of the beaker, making it equivalent to the case, when the block was floating and its weight was equal to the upthrust.
