The result of skill checks should depend on the intention of the character. For example, if a character has accepted a quest to hunt rats and rolls a perception check to look for rats then a high roll should reveal useful information on the location of nearby rats. If there happens to be some ogre footprints as well then a successful perception check to look for rats should not find that. looking for one thing and finding something completely different would be an appropriate result for a low roll.
Regarding passive checks, skills of an informational nature are generally always active and automatically succeed if the difficulty is trivial compared to the characters skill modifiers. For example, a character with a +5 perception modifier should automatically see a trap requiring a DC9 perception check to locate. They should not even need to ask for a perception check since the trap is so obvious and their perception is so good. meanwhile a character with a negative 2 perception modifier would need to roll to look for traps.
Skill checks and magic. As explained in the supremacy of magic lore article, magic does what it says it does. if some magical barrier blocks your path then you cant simply use an arcana check to bypass it. such checks are generally informational. For example, a character of the fey race is unable to reach a treasure chest protected by some barrier. A successful arcana check may reveal to the character that the barrier is in fact the magic circle spell which prevents certain races including fey from entering. Using this knowledge they could ask a party member who is a dwarf to open the chest since the barrier would not effect them.
Physical checks are straightforward. if a cliff is very steep then an athletics or acrobatics check may allow you to get over it for example.