Yes, it's different. AGENTS.md is a single file that is read by the LLM when the session starts. Skills are multiple .md files which are NOT read on startup - instead, the LLM harness scans them for descriptions and populates the context with those, such that it can later on decide to read the full skills/pdf/skill.md file because the user indicates they want to do something (like create a PDF) for which the skill is relevant.

Plus skill folders can also include additional reference documents and executable scripts, like this one here: https://github.com/anthropics/skills/tree/main/document-skil...