You don't have to use the area unit.
Of course you can.
PPFD and DLI are basically the same with the difference that PPFD is an instantaneous measure(each second) while DLI is a cumulative measure(over a period of time).
So 12Mol/m²/day means that at the top of your plants they are going to receive around 185umol/s/m² doesn't matter the size of your space, to get that amount of light you can adjust the power of your luminaire or you can raise or down your luminaire.