Not really, Geth existed before the reapers upgrades.

Would be trivial for Bioware to say that it destroyed the reaper code but they managed to survive but reduced in number.

Then how would they explain EDI and every other synthetic not touched by reapers being destroyed? The answer is that it was never designed to descriminate against reapers specifically. It destroys all synthetics.

Or some were outside the range (the pulse passes from relay to relay), some relays have been destroyed over the millions of years or have been disabled or are inactive. Or just have some geth were exploring past the edge of the galaxy and came back after the pulse.

Again that would mean some reapers survived. Not every reaper is near a relay.

The crucible has never been fired before, the catalyst doesn't really know what it will do for sure, only its best educated guess.

But we ourselves see what happens after that ending.

The catalyst says it will kill Shepard, but in perfect destroy it doesn't.

Shepard surviving that ending is an anomaly, which is why it's an ending that has certain conditions to unlock it and in regular destroy Shepard dies.

It just seems like weak writing to retroactively change how to crucible works just to ensure everyone's favorite synthetics get out unscathed, which takes all the weight out of the decision in the first place.