No, they don't show a scenario as Catalyst describes it, true. Yet the scenario is very easy to imagine. It's all in the terminology really.
Imagine organics wipe out all synthetic life in the galaxy. For synthetic life as a concept it's not the ultimate end. Organics can create new synthetic life, and may even do so for the exact same reasons they created it the last time. Now imagine synthetics wipe out all organic life. This is very likely the end of it. Synthetics may build their own synthetic servants (if they ever see the need) but why would they ever want to recreate organic (i.e. naturally evolving) life? It has no benefit to them.
It doesn't matter if the Geth would ever do it. It doesn't matter if it happens in 50.000 or 50.000.000 years. Once it happens, it's all over. This is what the Reapers are there to prevent. I based my whole decision to pick Synthesis on this simple thought. It's not necessary to drop an anvil on this issue, so I don't blame BioWare for not doing so.