I also noticed a clean output after the LPF with Phase noise as well, but I also noticed a lower background noise floor in receive, in fact I'm very happy with it now. If it wasn't for the hiss of the LM386, it would be a most quiet receiver.
Joel when you say noisier, do mean sounds noisier or scope trace is noisier? I built the top filter and I didn't hear any difference. On the scope, the signal cleaned up good, but I could see some phase noise.
I noticed that my receiver got noisier when I disconnected the built-in VFO and added the Si5351.? I get that a filter re-shapes the waveform, but I'm wondering about whether it's useful to clean the output signal a bit before injecting it into the radio.
I guess this is where the 'experiment' and 'learning' parts of the game happen. :)