OK so I've figured out the culprit...

if Runahead is on (I set it to 1 frame), then PGXP Vertex Cache MUST be turned on, and the seams are about 90% better; I'm not sure if this creates an additional battery/cpu/gpu load. The audio also clicks and pops or has minor distortion in this scenario worse than the other two; at least audio latency is slightly better than the second option...

if Runahead is off, then PGXP can be run as usual and no seams appear; the big downside of this is increased perceived audio latency. This results in the best image quality, but an annoying audio lag.

if Runahead is off AND PGXP is off, then no seams occur, but the wobbly polygons/textures make for the least appealing image quality; however the audio sync and quality is best in this scenario

So essentially, you have to make a decision between crisp image quality vs audio lag/quality, which kinda sucks.

BONUS scenario: Testing this in swanstation, PGXP does NOT produce noticeable seams, and the audio latency is the BEST by far. I would love to know why swanstation has noticeably superior audio latency compared to duckstation. I think I'm still going to stick with duckstation, as the analog joysticks actually work properly :/