The rules as written in the Cypher System Invisibility grants Specialization in stealth and Speed Defense rolls. However logically even a master of stealth isn't truly invisible and can benefit from actually being unable to be seen.
My own house rule is that Invisibility doesn't convey Specialization in the skill of being stealthy or on Speed Defense rolls, but rather one level of skill and one asset to both Stealth and Speed Defense. This means instead of a character being Invisible and having the option for two assets to reach the maximum four steps of adjustment, it means a character can only reach that maximum if they have some actual skill in being stealthy as Invisibility only covers the visibility of your person, not things like leaving tracks or how much noise you make.
Likewise Invisibility covers some of the same territory as a skill in stealth so the level of skill granted by Invisibility limits the knowledge and technique that a character Specialized in stealth can bring to the attempt, for instance someone invisible doesn't need to worry (as much) about light and shadow, which is pretty core to sneaking skills.
Shifting one level from Skill to Asset lets masters of stealth take some advantage of Invisibility, while limiting the ability of Assets to make something already completely invisible even more so.
Beyond Invisibility I take alternating levels of Skill and Asset as the norm whenever multiple step adjustments are granted by any one item or ability. For instance Concealing Firearms in the Firearms in Cypher System post, the Light Pistol grants a level of Skill and one Asset rather than two assets or Specialization in concealing it.
Note this applies when any one item or ability grants a two-step adjustment. If you have two items that provide one Asset each it still counts as two Assets, and a third Asset won't actually help. A single item or ability that provides two steps of difficulty modification is powerful enough that someone highly skilled will still be able to get some benefit from it, while someone with limited skill will have their deficiencies in knowledge or tecnique covered by the item.