Coal is fossil land life. Seas rise and fall (and rise) during geologic times. Likewise plates move, mountains form, bays get buried. So yes, some coal is now found below present day sea levels, but it started as swamps and forest. The fossil imprints strongly indicate that, i.e. petrified wood in the coal on the NSW coast. For more details I highly recommend the series of books by Mary E. White on paleo-botany of Australia with particular details on the East Coast fossil fuel formations.
By the way, most remaining Australian coal is energy negative to produce. A similar situation exists with respect to shale oil. Takes more energy to get it out than one can get out of it. May be useful in the distant future as a chemical feedstock but not for burning it to get energy.
