Those pictures don’t look terrible. I have a clown goby that’s been through complete qt and is 100% healthy. He eats Hikari frozen mysis and LRS reef frenzy. They have a sculpted look to them that gives the impression that maybe something is wrong. They also contort their body to suction to vertical surfaces which gives the look of boniness.
If your clown goby looks like this, something is wrong with it. Look at the lines around this one's face. You can see every outline of every angle in his skull, his spine is sticking out- that is not a healthy body weight for anything.
There's a healthy weight clown goby
https://plugon.us/fishtank/citron-clown-goby-1348e here. See how the body is smooth, without any of the angles of the bones visible? They're not supposed to have a sculpted look, they're supposed to be smooth and rounded, with maybe a tiny hint of a ridge in the face from some angles.
That fish is not built this way. That fish is missing significant amounts of, not just fat storage, but muscle. This is a severely emaciated fish, that I'm honestly surprised is still kicking. The feeding is probably helping- keep up with that, though maybe cut out the brine, that's not very nutritious. Mysis shrimp is good. Maybe try canned cyclops, or see if you can get any fish eggs- something fatty.
Phytoplankton can help to grow copepods, and is good for filter-feeders, but isn't directly relevant to the fish. They don't eat it.
And, no, parasites from one fish wouldn't necessarily become particularly symptomatic in the others. The others would probably catch them, but a healthy fish can live with intestinal parasites and be fine, until/unless something stresses them and gives the parasites the upper hand.
If you're certain you're seeing normal poop from him, you might be looking at organ damage from cyanide collection- I've recently learned that's very common with clown gobies.
You may want to look into anti-parasitic medications regardless of normal poop. Something is clearly wrong, and it may be worth trying to treat for parasites, just in case.