Not is "almost" done, is done.That ship's bar goes all the way to 100%, and there's even a little green "completion" indicator at the end of the chart. This is one of the major arguments showing that Jein's number assignment is wrong. He assigns that number to Intrepid, but that ship is complete and would therefore not have repair crews still working on it, so that ship cannot be Intrepid.
You are right. But if the ship is done, why does it still appear on that chart?
Because the ship was still present at the base, and 100% complete is still a status? Presumably the portmaster would still need to know what ships were physically present, even if no further work on them is required. (Besides, when you're doing project planning IRL, when you finish a task, you mark it as complete on the plan, you don't just remove it!

There's one major issue I have with this chart just showing repair performances at this starbase.
According to the context featured in "Court-Martial" the Enterprise has just recently arrived and Kirk apparently hasn't been to the starbase club, yet.
To be fair, going to the club probably isn't going to be one of his highest priorities!

Yet, the chart clearly shows that there has been considerable "completion" progress on the Enterprise!
Considering there are three to four more days coming before repairs are complete, this "repair status" chart would then indicate that Enterprise had already been there for over a week!
I'm taking the following from the episode transcript at chakoteya.net, since I don't remember the dialogue from the episode well enough from memory.
From the dialogue, we don't really know how long Enterprise has been at the starbase. Kirk's intro log entry mentions that a full report of damages was made to Commodore Stone, but that seems to be a previous meeting, since the purpose of this meeting seems to be to review Kirk's deposition, which was probably taken earlier by a JAG officer at the base. Stone reassigns a repair crew while he's waiting for Kirk, but nothing says this is the first crew assigned to Enterprise. There could already be personnel working on Enterprise, and Stone added section 18 in to help. So we don't know how long they've been there, and there could already have been repairs in progress by the time the episode starts.
And I'm not sure where the "three to four days" comes from. The only time I found an estimate was when Kirk mentioned in the bar that repairs would take a "couple of days".
(OT: I know trying to make sense of TOS stardates is a fool's errand, but here's how things seem to go according to the stardate references in the episode:
2945.7 - Finney dies
2947.3 - initial log entry
2948.5 - full repairs in progress
2948.9 - repairs almost complete
The repairs aren't mentioned after this, but there are two more log entries during the trial at 2949.9 and 2950.1.)
There's one fairly simple solution to this, which happens to be how I've always thought about it anyway...
I've always liked to think of it being more like a "health meter" for any ships present at the starbase - here are all the ships present, here's the level of functionality on a 100% scale. I've never felt that the bar accurately represented how much work had been done, inasmuch as how functional the ship was.
I actually like this theory, but unfortunately it doesn't mesh well with the "% Complete" header. ("% Operational" or something would fit better.) Your theory also has the advantage of being a more meaningful graphic. For example, using this theory, you can see right away that, say, 1701 is in better condition than 1703. "% Complete" suffers as a meaningful chart because you don't know how long the repairs are estimated to take. So if 1701 is at 83%, but her repairs are scheduled to take two days in total, she's a lot further from completion than 1703, which is only at 51%, but whose repairs are only scheduled to take, say, four hours.
Or maybe I shouldn't be analyzing set decoration too closely!

In which case NCC-1700 has taken a whoopin.![]()
That's what happens when you don't have Jim Kirk in command!

Hmm, that theoretically could work. Is there a visual catalogue for the plaques on other lead ships?
Well, of course we never saw any other ship types (or plaques of said ship types) in TOS itself. By the movie/TNG era, for the lead ship it looks like they used the text "First starship of her class" instead.
Excelsior
Defiant
Prometheus
I can't remember any other lead ships we might have seen, off the top of my head...