Every solution is a lock-in. The only way to be free is to do not note anything at all. But then you are locked into the liberty of nothingness.
Note-managment on surface is simple, but in the long run in becomes quite complex. At the end it's not all about data, but also how you access them, how the system handles them for you, how you get them presented, etc. There is low-level stuff like syntax of markup languages, and also high level stuff like tooling for displaying and automation of your data. Languages like org-mode or markdown have quite the high level of syntax, with simple things like text-formating, more advances stuff like tables, links, internal links, and high end stuff like codeblocks, metadata-handling.
And then you have tools like org-agenda or org-babel who work on those features (not sure if markdown has those too), and you build your workflows and life around using those tools, and at some point you are so tangled into an complex environment, that any fundamental change would cripple your abilities you have build over years significantly. And then you are locked-in, even if your data are free and open.
At the end, your set of tools, the workflows you have build with them, the experience you have aquired for specific domains and the habits you developed over the years are your cage that prevent you from moving on to different systems.
Org-mode has many such features, tools and habits you imprison you. There is org-agenda, org-babel, internal links, headline-tags, todo-tags(?), but also the outline itself. Those are the usual popular tools and features, and they are not much used in other systems, and hard to convert when you aim to move out.