Remove redundant ClimaAtmos checkpoint

[Sbozzolo]

#1179 introduces checkpoints for ClimaCoupler. As implemented in the PR, ClimaAtmos produces two checkpoints at the time instead of one. The reason why the choice was made is that ClimaAtmos does not provide a simple way to start a simulation from a time that is not 0, except when restarting from its own checkpoint. So, in order to have aligned times between component models, the simplest thing to do was to pick up from the previous checkpoint. The better solution for this might be to simply allow for a different t_start in ClimaAtmos.