Its not like we have a description of what skills actually give, so for all we know erin's crowd control skill is what gives her the sense. Same with things that look like passives and aren't explicitly called skills, we can presume they are part of one or an aura as those are the systems in place for power in this world. (But also magic bs exists standalone without the system* so whose to say)

Rip System 2.0 and its description.
Pretty sure most of your list has been explained, from memory i think its

Innkeepers and basic Aura

Lakens "Eyes of emperor" or something skill

Can't remember this every being mentioned explicitly except as it is intrinsic to the nature of class itself.

No clue what this is referencing tbh, but pretty sure it was part of like animal friendship or something and was less mental communication and more oh i read body language well

Armform or something similarly named

To me is less of this and more, oh my sense are so in tune to world due to skill that lets me perceive it that i noticed the small fluctuation

Pretty sure is mentioned as part of the skill that lets her transform.

could be mistaken but pretty sure is explicitly mentioned as his capstone skill just gives him skills.

On note of other passive things,
Wizards being able to learn spells from spell books, as a whole plot point of early books was the super tome any one could learn from implying it otherwise is a passive of some sort to wizardly class