Hi - try the dB threshold setting to leave out quiet grains. With normalization on, that can give you bad results because low level noise ends up being boosted, making the grain appear "bright". Another problem is that a fixed window size will always get you audio slices that have mixed content - with a window size of 93ms, it's pure luck if you get a speech grain that only contains "aaa". It'll likely have a little "sss" or something else in it too. So the solution there is to try to parse the audio based on content, not size. And using single value features (like brightness), BFCCs, or Bark spectrum, you're fine to compare grains of various sizes - the length of features like BFCCs/Bark spectrum depends on the size of the Bark filterbank, not the window size.
About phasing...the worst case is that you end up overlaying the same grain with itself, but offset a bit. Don't know if that's an issue in your case. There is the "stutter_protect" option in timbreID to avoid repeated grains for concatenative synth, but I think you're just doing ordering? Anyway, it's a major problem with this technique, because the goal is to spit out sequences of timbrally similar grains. If things are working properly, that will always produce sequences of grains that have similar waveforms, and if you overlap similar waveforms, you get phasing/filtering! To be honest, I've only ever done two things: 1) add low levels of good reverb to smooth it out. 2) add controls for randomizing the grain size within reasonable bounds (like 90% - 110% of the window size). That at least varies the otherwise steady windowing artifacts, which can turn into a very audible flutter if your output overlap is high.
One other thing to be aware of: if you do the analysis with a high overlap factor, you're more likely to overlap identical content. So an overlap of 1 is best from that perspective, but then you lose time resolution and end up with fewer grains. Or, taking things back to the first point above: if you have good segmentation based on content and not a fixed window size, you're less likely to have extremely similar waveforms overlap and cause phasing. With a reasonably small audio source (like your Lucier content), you could do this manually with labels in Audacity. Takes a lot of patience but I bet it would make a noticeable difference.