Electrical – Are all ground wires inside electrical junction box grounded

The silver wire is also a ground. Chains are not grounding paths so a pendant needs 2 grounds - one down the chain to the pendant, and the other for the box cover.

I suspect the manufacturer ran an extra run of 14/2 (12/2?) Romex from the switch to support a ceiling fan which you don't have (yet). I bet the third black is folded up in the back of the box, but they tied this pair's white wire with the other white wires. That's making my spider-sense tingle, but I can't say why. Might make a good question.

Since the power is fed from the switch (no weird switch loops) you should be able to connect all blacks to each other, ditto the whites. All grounds must be connected together. I don't see any obvious way that upper steel plate bonds to the maze of ground wires above it, and that makes me a bit nervous. Is that a steel box above, and is the ground bundle bonded to it in some way? I see a screw, but it's not green and may be a physical mounting. Is the steel cover plate tightly screwed to the steel box?

As far as wire-nuts, each make of wire-nut is listed for certain combinations of wire. For instance Ideal's 73B (orange), 74B (yellow) and 76B (red) are covered in a document titled UL Listed wire combinations... Generally I like to be in the middle of the working range for a wire-nut, so I'd go yellow for 3 wires, red for 4, and orange for something that seemed on the smallish range for yellow.

In a single circuit, all ground wires and metal fixture structural parts are connected.

In your case, the green wire is the ground for the lower part of the fixture. The bare wire is the ground for the metal canopy. The green screw is the ground for the fixture bracket. The bare wire buried under the bracket is the ground from the circuit cable.

They all need to be connected. The easiest way is to attach a short bare (or green) wire to the green screw and then attach the four ground wires together.

I prefer the newer push in connectors for solid wires (they can be used for stranded but are a bit harder to use). Or you can use a wire nut. Just be sure to strip enough bare cable to get a good twist on all four wires before putting on an appropriately sized nut. Most practitioners use a lineman's plier to get a good twist on multiple wires.

Never put more than one wire under a screw or nut.