It’s been the case ever since KI launched. Enders must be cancels (after an auto-double, linker, manual, etc) and they must be on a grounded opponent (ie, someone “in the combo sequence”). Since S2 has some characters that like to do juggles, they added a special rule starting in S2 that let shadow enders cash out as enders any time they are used as an ender, including on juggled/mid-air opponents. This means that if you want to cash out an opponent who is in the air, you MUST use a shadow ender or you must recapture them in order to use “normal” grounded enders.
To put it more succinctly, moves marked as “shadow enders” will cash out when used as manuals (see below).
The word “manual” is just KI-speak for “link”. You can link two moves together any time you can fully recover from the first move and still have enough time to start the second move before your opponent has left hit stun. So… the “manuals” that you are used to (normals used in a combo after a linker) work with this definition. You do the linker, wait for it to completely finish, then try to hit with a regular normal. I’m sure you’ve noticed you can also do (light) manuals after heavy auto-doubles? It’s because there is enough hit advantage for the link to work.
This also applies to air-to-air or ground-to-air juggles. If I launch you with Jago’s laser sword ender, then walk up and hit you out of the air with anything (a normal or a special move), this is a link, so calling it a “manual” is accurate. If I anti-air you with early light DP as Jago, then do another DP before you hit the ground, this is also a “manual”.
You can do “special move manuals” even when both of you are on the ground. It’s rare, but it’s possible. For instance, Jago has a super fast DP, and light laser sword opener leaves you with enough frame advantage to do an extremely late DP. If you wait long enough between them, you won’t get the ender version, instead you’ll get the DP you would normally get in neutral; it won’t cash out because it’s not a canceled ender, but it WILL be combo breakable if you guess the strength because you have done an opener somewhere in the combo before it. It’s effectively no different than doing, say… standing MK as a manual after light laser sword opener (except st.MK will let you keep going with the combo sequence, whereas a DP manual just ends your combo).
He doesn’t really have a “true” damage ender, no (that is, an ender that does remarkably more damage than other enders with no other added benefits). But every character has an ender that does the most damage they can do, and it just happens to be pulverize for Aganos. So I guess you could call it his “damage ender” if you want.
Eh, Aganos players are rewarded for lockouts. They can get 3-4 chunks for free, and if they want, a ton of corner push with shadow natural disaster. His reward “looks” a little different because it doesn’t say 60% damage under the combo, but he definitely gets rewarded in ways that help him win matches.