Making miso in a jar too big for the amount of paste. Is it a problem?
I have been into miso for a short time, so I am far from being an expert and I won't attempt a complete answer. However, let me raise two points which I think are relevant:


It is common to remove and dispose the thin dark layer that was in contact with the air when harvesting the miso. The reason is that LAB bacteria present in the air often proliferate on that layer, yielding a rancid and acid layer of miso which you are not looking for. A larger pot will likely have a bigger surface cross section which will yield a bigger layer in contact with the air. In other words: putting little miso in a large pot will yield you less finished product. In my opinion it is a pity to think you will be throwing away a good proportion of something you waited months to make!
According to the Noma Guide to Fermentation, you should put a weight of about 50% the total mass of the miso during the fermentation process. I believe that what is really relevant here is not the mass on the top of the 'miso cake' but rather the pressure exerted on cake. If that is correct, using a big pot for a small cake will probably require you to put more than 50% of the cake weight in order to get the same pressure 50% mass would exert in a smaller pot (and in the extreme case to distribute it well accross the surface).


Maybe you have already crossed these videos, but if you have not I recommend watching this, this and its follow up to see the recipients and weights they use.