It doesn’t matter if you just have launched Renoise and loaded the song or if you’ve played the song right before, the rest of effects can always be heard at the beginning of the song, regardless whether it’s an empty pattern or if you start with a full pattern right away. This has always been an issue, so there’s no way to avoid cutting the rendered wav at the beginning externally. At least not for me. This is not a “what you hear” issue, the first pattern is always treated like the last pattern just has been played.
Well, it takes 10 seconds… You’re spending hours or even days for mixing and mastering, so spending 10 seconds to cut a wave properly really doesn’t matter.