Thanks.

I haven't gotten that far, so I don't know for sure, but it's probably because they are really powerful skills and/or toggle skills (IE skills that only ever have one point because they are ether on or off). Take the one in the list for example: Poison Coat Jewel 3. It lets you use Poison coat on a bow that normally wouldn't be able to. That's a pretty big deal.

ive only gotten 2 lvl 3 decorations so far which was for flinch free and earplugs. both strong perks so most likely the lvl of the decoration is not about how much skill point it gives but rather how strong the perk itself is. maybe weaker perks like buff atk, buff elemental dmg etc. get more skillpoints with lvl idk

The skills that take 3 slots but only give 1 point are generally powerful skills that are worth more

You get them at random high rank quests rewards

you get them as safe reward from tempered monster quests in late game. i usually get 3-4 per investigation (depending on the investigation bonus slots)

can you put the missing ones in the list on in your comment please ? I'm searching for some decorations and I don't know if I'll ever find them (and farming Tempered Vaal is fun but can we get all the skill on one monster or is there some specific skill for specific monster ?)

It's called Critical Boost, it's up near the top. Haven't seen rapid fire yet.

Well we don't know yet if there is or isn't one. The game has only been out offically for 2 weeks

The skill points should have been added to your skill list. Maybe try the total skill list rather than just the per piece of equipment one.