I don't believe the performance difference between Cranelift and LLVM really has much to do with E-graphs. Cranelift had this same performance profile (faster than LLVM but generating slower output) before they switched to E-graphs.

Rather it's about how much effort Cranelift puts toward optimizing its output- it has fewer, less involved passes (regardless of whether those "passes" are expressed as part of the E-graph framework). More subtly, this means it is also written to generate "okay" code without as much reliance on those passes- while LLVM on the other hand generates a lot of naive code at -O0 which contributes to its slower compile times in that mode.