So I am loving the Molecule library for doing complex stuff with collecting multiple flows and emitting new flows. However, the code wise overhead is so small and the mental benefits, for me, are so much better then complex flow operations that I want to use them a lot. Is there a large overhead in starting a compose runtime for this?

Benchmark it. That's the best advice I can give. There's gonna be a little bit of overhead for everything you do, but what matters is benchmarking it and seeing how much it really matters. Use Kotlinx-benchmark