I do not know, maybe I play it wrong, but I feel a little bit lost.

I'm just walking from place to place, doing missions for random NPCs and it is all nice in terms of gameplay (sneaking, fighting, jumping and climbing, finding secrets, hacking stuff, etc.), but I feel like...It is hard to say... like I'm out of place, like I'd jump to advanced part of story without doing something basic introduction.
Each and every mission I encounter seams to be of equal importance, yet some are walk in the park while other, not far away, are a suicide.

Is that how open world games should be or is there some order of playing I accidentally missed and now should start all over?

To get back on track I tried to do main story but... not to spoil too much... the moment into his mind, I just have to fight... it seams a bit too hard, especially I did not intend to fight anywhere else, but rather run and hide.
Does that mean I get there too early or I missed some important fact that would let me skip that fight?

Any clues, hints or suggestions on how to properly play are welcome.

Judging from your description I think you're playing it (more or less) as intended?
Open world games with such a high degree of freedom are usually designed around that and there's actually no wrong way resp. order in approaching and advancing in the story, especially when it's made crystal clear which quests are just on the side and not mandatory for story progression.

I actually found it quite similar to Elex (to name a recent game with a similar approach to open world design), where there's also a somewhat hidden but quite clear distinction between main and side story content.

And I don't think that you actually can ghost Seven 100%. If I remember correctly, all of the bosses can only be overcome by fighting them in open combat. No skipping or beating them without use of force or violence.

Yeh, it seams that it is not possible to avoid fighting.
I used other weapon, applied some mods from crafting, found some more skills and found out how to set them up. After that the fight I had problem with was a breaze. In fact that was a turning point - said weapon and skils served me well till the end of the game.

But despite 40 h of play time (at home on a sick leave) I guess I'll have to start all over anyway. I'm still not sure if that was intended that I finished the game or I just was unlucky enough to encounter some bugs of unpatched version.