That's where encoding in in RNA would be important, think about just a monotomically incrementing clock tick from one virus generation to the next, two cells would only merge if they had the same clock.

I basically know nothing about what's possible in RNA/DNA, but my understanding is that RNA can be used to adjust DNA, which could essentially increment a clock tick.

Not an expert but I suppose it's sufficient if you model the virus such that an eventual equilibrium is (or contains) your solution.

That's some serious hand waving.