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(Adam, Thingsquare CEO here)

Yes, the 100 nodes in close proximity is quite a bit different from 100 nodes spread out across a larger geographical area. Even if we can play tricks with routing tables to make the testbed act more like a real deployment, there is much more congestion in the testbed because all can hear each other. Also, there are many wireless effects in play in a real-world situation, such as the capture effect, that has several implications for how the distribution and routing protocols operate.

By default, the simulation does not try to replicate the testbed setup, but rather the real-world deployments. But we can tweak the simulation to behave more like the testbed if we want to inspect behavior we see in the testbed that we don't see in real-world deployments.

(As it happens, this was pretty much the topic of the PhD thesis of Thingsquare CTO Fredrik a few years back: http://uu.diva-portal.org/smash/get/diva2:447343/FULLTEXT01....)