So now that there is a new type, I have a suggestion for all five cards, because I think it would be better and cleaner if they worked the same way.
As I said earlier in this thread, I think they should all say non-Duration, or we can just live with the lack of tracking for these cards. But since Donald is obviously going to stick to the special tracking rules for these cards, I think it would be better to make them all consistent.
The new rule ("2. Tracking for the former shapeshifters") mentions all cards - Band of Misfits, Overlord, Inheritance, Necromancer and Captain - but actually doesn't currently apply to the last two, since they already say "non-Duration" and so cause no tracking problem. This rule also presents the challenge (mentioned earlier) of defining which cards it applies to without including cards like Throne Room. This can be fixed with awkward wordings.
My suggestion is to add the Command type to Necromancer, and change Inheritance so that Estates also get the Command type; and then drop "non-Duration" from Captain and Necromancer. Now all five cards work the same way, they can play Durations with the exact same tracking, and they can't play each other. And the tracking rule can simply refer to "Command cards".
Rule 2 is there to tell people about the changes; the actual rulebook location for rule 2 would be in each relevant card's FAQ. It wouldn't have a special section in a rulebook because it's not something I want anyone to see unless they are specifically looking up a relevant card. There's no challenge of which cards it applies to, it would apply to the cards that explained it. It's not challenging to me either, it's cards that play cards that aren't put into play. Throne Room for example does not do that; it can fail to put the card into play e.g. when playing a one-shot the second time, but it always tries to put the card into play. I guess we can say, do we count Scepter and Royal Carriage, which only play cards already in play; their tracking is already covered and I wasn't defining new behavior for them.
The problem with consistency here is loud voices on the internet complaining about cards losing functionality. If I were making the cards all from scratch, new cards for new expansions, then I mean I would fix them up every way I could, I would avoid having a phrase like "non-duration, non-command Action" (even though Magic has done that on commons from the beginning, I am just mentioning that due to the injustice of having this be compared to substance) and so on. The direction of "give them a type and exclude it" is not an unreasonable approach, again for the situation of making these cards for the first time ever; it makes sure you don't have a problem. If I get to go further back and do e.g. duration cards and one-shots differently, well in addition to probably doing something like saying, duration cards don't function if they aren't in play (and notating that well), odds are I wouldn't do Band of Misfits, because I would want effects to be tracked better than it can manage.
But, the actual situation is, I made some cards, and have to live with them; even if a future version of Dark Ages replaces Band of Misfits, the card exists and needs rules. And again there are those loud voices. It's no surprise that people don't like to see combos go away, even if they'd never miss them if they'd never had them. The ideal fixes are ones that change as little as possible.
Thus, not adding Command to Necromancer, which didn't need it. For Estate, that's more borderline, and I can reconsider it when actually reprinting Adventures. Putting the type on Estate is cumbersome on the card text, but adds extra protection, as demonstrated by, if we drop "once per game" then you can Inherit something and then Inherit Estate, which is bad.
Similarly I initially thought Band of Misfits would get non-Duration. People were happier with that not happening. We have tracking for that situation and so it doesn't say non-Duration. In the best of all possible worlds, I just don't do the card; in the weird nightmare world where I have to do Band of Misfits but get to change it before it goes to print, and can't just make it e.g. "choose one: village or smithy or something," well, I would consider non-Duration. I'm not in that world, I'm in this one, where people are used to Band of Misfits working on Duration cards and would be sad if I took that away.
I do agree that it would be nice if the rules could just mention Command cards.
To sum up! It would be nice if the cards all fell into line more; they don't because I care more about the players being happy than about the cards being their prettiest.