How do I stop the black seed beads from blending together in my papaya brooch?

Black on black will always mush together up close, that's just how the eye works with a solid dark cluster. What actually makes seeds read as seeds in a papaya centre isn't pure black, it's something with just enought life in it. Gunmetal, hematite grey, or a very dark purple all look black from arm's length but catch light differently bead to bead, so you get separation without the centre looking wrong. If you don't have those on hand, even mixing a matte black with a glossy black helps a lot, since the shiny ones throw little highlights and the matte ones sit back. You only need two finishes for it to work.

On the thread question, don't just accept it. I've been doing this since we all stitched on felt with doubled-up sewing thread, and switching to a dark thread mid-piece was standard practice even back then. Wind a bobbin of black or dark grey and use it only for the seed section. Also run your thread over a block of beeswax like the old-timers taught me, it tames the shine so the nylon stops catching light against those dark beads.

For the spacing, try a bit of stitch tension variation instead of moving beads apart. Some seeds sitting proud, some tucked down flat, breaks up the cluster without thinning it out.

Made a watermelon brooch last summer and hit the same wall with the seeds. What fixed mine was staggering them in a zigzag instead of neat rows - real papaya seeds sit all wonky anyway, so the uneven spacing gives your eye something to grab onto even if the color's flat. Rows make them read as a solid line, wich makes the blob effect worse. Also, before you redo anything, snap a photo of it and flip it to black and white on your phone. Weirdly helps you see which beads are actualy separating and which ones are blending.

The zigzag point from the watermelon post is exactly right. When I did a passionfruit brooch I had the same blob problem, and mixing two sizes of the same dark bead sorted it out. Mostly size 11s with a handful of bigger ones dropped in at random, and the bigger beads broke up the cluster so your eye stops reading it as one mass. I didn't even need a second colour for it to work. It also meant I didn't have to space them further apart, so the centre stayed nice and dense like it should be.