Great question, baskapteijn and Christopher Demicoli. iPerf3 will run natively inside of WSL2. There are no emulation issues there.
But... the WSL2 network traffic will traverse either the NAT or mirrored network subsystem inside of Windows. These are software network layers, which means additional latency and possible performance limitations will be incurred on the WSL2 iPerf3 traffic.
So please keep in mind that the iPerf3 results from within WSL2 will not be the same as Windows native ntttcp/ctsTraffic results. Using iPerf3 in WSL2 would measure WSL2 network performance, not Windows native performance.
WSL1 is Linux syscall emulation on Windows. iPerf3 will kind of run natively, but all the syscalls are emulated. iPerf3 should work, but I have not personally tested it.