Ion beams do not do well in penetrating the atmosphere–they are stopped very quickly. As people pointed out in the Star Wars days, there are lot of problems in using them in space as well–earth’s magnetic field for one.
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> Second, assuming an ideal Focus Fusion generator, how much of the power
> output comes out as heat? Which is to say, in a system like a spacecraft,
> where getting rid of heat is critical, how much of the 5MW from a 5MW
> reactor is going to try to cook my astronauts?
About equal, around 5 MW. Getting rid of the heat is the biggest problem for space applications. Since cost is less of a consideration part of the heat might be used for power, which on earth would drive the capital cost way up, but might be less massive than the heat radiators.