How far into a footing pier should rebar extend from the rock below?

Well, if it's poured & done, you're evidently into the test phase, so this is not really going to help you much unless it fails and you replace it (which seems unlikely.)

Normally you want rebar a few (2-3, depending on conditions) inches deep in the concrete (for corrosion resistance) but otherwise as near the edges as practical, and connected to as much of the mass as practical.

The basic spacing sounds reasonable, but the fact that it's all within the footing is less than optimal for the pier. There are probably few tension loads on the pier, so it's likely to be fine - you've got the footing attached to the bedrock.

Normally you also want to "cage" between your uprights - tying the bent-over bars in the middle is probably doing the least they can do for you, but you didn't cut them long enough to bend over and reach the next corner, and you don't mention bending and tying any other rebar in that position, or adding mesh. Whether doing a single pour or two pours, it's good practice to have rebar sticking up from the base into the pier, though your pier is rather short. So having it stick up 4" when the pier starts at 5 inches and tops out at 9 inches is less than ideal.

When anchoring to rock, I prefer to drill at slight angles so the rods cannot be pulled straight out as a set once the concrete is poured, regardless of epoxy or grout holding them in the holes.

In order to develop full bonding capabilities between concrete and rebar AND to protect reinforcing from corrosion and decay, the ACI (American Concrete Institute) requires a minimum of 2” cover in normal conditions and 3” in corrosive atmospheres. (See ACI 318)

That is to say, where you live you need a minimum of 2” between the rebar and ground, which it sounds like you have 4”. In addition, you need a minimum of 2” cover over the top of the rebar and along the edges of the footings.

To answer your question, the rebar needs to extend a minimum of 4” (plus 2” cover) into the rock. The 5” holes with rebar is for lateral movement. A #4 rebar in each hole will adequately resist lateral movement if the rebar has adequate concrete coverage. That means the vertical rebar needs to be exactly in the center of the hole.

I’d keep the holes drilled perpendicular to the rock, rather than drilled at an angle to keep the concrete from “bouncing” out of the hole no matter which way the concrete (load) moves.

Rock has such high bearing value that the 18” x 18” and 20” x 20 footing will hold up about 100 cars. This is plenty adequate for your deck.

However, the weak link seems to be the connection between the concrete footings and the wood beams for the deck. You’ll need a steel connector set in the concrete footings during the concrete pour.