TLDR: I personally think the best way is to get a cutting and grow it out for 2 years and then visually it should be obvious.
There's a bit of a myth that the two are indistinguishable. When grown outdoors (parks, forests) etc. the two are easily distinguishable, mostly with the peduncle, diameter of the fruit or leaf size. What is rarely debated is F. rubignosa and F. obliqua, which is identified as a complex in published literature. No such complex is recorded for MBF and PJF.
The problem we have is trying to distinguish the two species when they are grown in pots. It's noted that there is a lot of variance in the species PJF; it needs to be mentioned again, that variance doesn't mean that it is indistinguishable, which often gets said. But it does make it harder to accurately identify unless we can find something to measure against.
For anyone that's worked with a few, the difference is usually obvious and you can tell just by looking at the tree. MBF is just bigger - typically bigger leaf size, typically thicker petiole, typically longer petiole, typically longer stipules.
I personally think the best way is to get a cutting and grow it out for 2 years and then visually it should be obvious.
(below) This is my noodle cup MBF, it's only 9 months old and leaf size only needs to be 2cm longer to exceed PJF maximum range.
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The problem I have with petiole colour is that MBF aren't always red (see the example photo I posted previously in this thread). Also, PJF petiole can also be red.
(below)PJF with red petiole, however petiole length across the tree is less than MBF minimum length. This is not a MBF.
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The problem I have with leaf shape is that there is a lot of variance in leaf shape and colour for PJF. I have one example here which is almost yellow and it's nearly diamond shaped.
In print, this is what we have to go by:
PJF
Petiole 7-82 mm long, 1-4 mm wide, glabrous or
minutely puberulous to pilose, with ascending hyaline hairs which may or may
not be interspersed with weak ferruginous hairs, glabrescent, or with weak ferruginous hairs glabrescent.
Lamina 30-193 mm long, 12-132 mm wide;
Stipules 23-130 mm long
MBF
Petiole 31-88 mm long, 1-5 mm wide;
glabrous, or pilose with ascending hyaline hairs interspersed with weak
ferruginous hairs, or with ascending hyaline hairs, glabrescent.
Lamina 70-297 mm long, 39-125 mm wide;
Stipules 70-146 mm long,
In practice, you can build enough ramification into a PJF to get a stable leaf size below 3cm. You can't do that with a MBF. I also find MBF really hard to grow from cuttings and almost 100% strike rate with PJF.
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They can be tricky to pick sometimes, so all these tips are helpful 
worth of extra advice if you are not sure which to go with. In my opinion the Moreton Bay figs make better bonsai if you are prepared to constantly reduce the leaf size. They are both incredibly hardy, but I find the Moreton Bay fig is just that little bit hardier for drought tolerance and over watering. But this last paragraph is obviously just my opinion.
but looked a bit closer and I can see the mid rib starting to turn.
