1) TA was already 3D since it's 1997 release, only, the camera was fixed, and the map rendered like a huge bitmap, since with a fixed camera there was no need to use textured polygons for the terrain that would always be seen at same angle. But already in 1997, TA units were little 3d mapped models, shots trajectory were 3d, each units and shots had an altitude, etc... The game inner mechanic was in 3d, just only half of the rendering was 3d.
In 1999, the Swedish Yankspankers released the 3d replayer, which was an addition to their previous work, the TA demo recorder, and that 3d replayer made it possible to view a TA game in full 3d with a free camera. Totala.exe would still be running and "playing the game", but that TA3D.exe was... I don't know what it technically was exactly, but it felt like a alternate rendering application that just made it more glaringly apparent TA was in 3d, since instead of a fixed view, we had a camera we could move and turn freely. You can still find the 3D demo replayer at
http://www.clan-sy.com
In 2005, the Swedish Yankspankers released Spring, which was not just a 3D camera mode for TA, but instead a whole new engine, that just happen to be compatible with TA data format. That means this time they coded everything, the collision, the pathfinding, the interface, the whole underlying mechanic, and not just a 3d render.
Technically, Spring is a new RTS engine that has nothing to do with TA. However, because developping the content (hundreds and hundreds of unit models, of unit animations, of weapons, of textures, etc..). is such a huge work, and because Spring can read the same data as TA, most modders went the lazy way and simply reused TA data instead of making their own. Also, for historical reason, many people are used to TA units and aren't willing to try novelty, or keep thinking (just as you do) that Spring is merely TA in 3D, or any other reasons, but TA based mods remains the most popular.
2) Saving a skirmish is not possible currently. In some early version, there was a save key. Also, recently a mysterious contributor has submitted a patch that allows saving and loading even with AI, and hopefully it will be included in the next version of Spring.
Also, since you mention skirmish, keep in mind Spring is mostly multiplayer oriented. Single player is possible, but it wasn't the developper priority, so it's not as easy to get it working as clicking a "single player" button like in any other RTS. If you look hard on
http://www.unknown-files.net you can find AIs, single player battleroom, and even single player missions, but installing them and getting them to work can be a pretty rough ride for a newbie.
3) The question is irrelevant once you start to realise Spring isn't just 3D TA. But everybody who made a Spring mod with TA units started with the Cavedog official unit set, including Core Contingency, 3.1c patch, and the 6 last units. Then proceeded onto removing units, adding units, or tweaking units. But no one ever even talked about doing a TA 1.0 mod without the add-ons units. So uh the answer is yes, Krogoth and the like are in. Though in reality it's all at the whim of the modder. The people who work on the engine, aka the developpers, are a separate bunch from the people who works on the content, aka the modders. Most modders reuse Cavedog's unit. But some, such as Smoth with Gundam, Fang with Expand & Exterminate, Argh with Nanoblobs, SpikedHelmet and his minions with 1994, KDR_11k with Kernel Panic and his other dozen mini mods, instead developped their own content, without reusing any TA units. So no Krogoth in
Kernel Panic for instance. Did I tell you to try
Kernel Panic and
Gundam? If not I tell you now: Try
Kernel Panic and
Gundam!
4) I don't understand the question.
5) Yes it is.
