With the next version of Spring, it will be possible for units to "take cover", at least kind've. How gets into technical areas of scripting that you're going to need to have a lot more background knowledge on before you're really going to understand it.
Having multirole troops that only fire at set target categories is completely feasible. And, so long as you're aware that Spring is not a "war simulation", but is a game made for contemporary RTS gameplay, you can have pretty sophisticated units, and this is likely to get even more interesting as things move forward.
In short, so long as you're not looking for a RPG-like game or a detailed, exhaustive simulation, Spring is great. But, from the sounds of the games you like, you're almost entirely focused on the single-player experience.
If that's your focus... well, the short and honest version is that you'll be breaking a lot of new ground, on a technical level, and you may want to get it working for simple MP play first, so that you're not trying to bite off more than you can chew. I don't get the sense that you have a lot of prior experience with all of this stuff- for example, have you ever done 3D modeling for games before? If not... you have a 3-9 month learning curve ahead of you, depending on your desire and free time. Again, just being real- there are a lot've things with game design you don't just read a simple tutorial and suddenly become fluent in
Building single-player missions with Spring, via LUA scripts, is at least technically possible at this point. However, I haven't the slightest idea just how much interactivity you can add to them, and I daresay that almost nobody else (even the coders who wrote it) really has explored this much. There just isn't a lot've interest in the Spring community in single-player scripted missions at the moment. This is not to say they're bad, or that we won't cheer you on, but if you really, really want that kind of gameplay... you need to understand that there just aren't any people available to answer most questions about how to proceed, and that a pretty thorough grounding in LUA will be necessary to achieve anything more distinctive than a set-piece kill-em-all sort've thing.