I think this is a very important point and one that people should take into account as they structure the way they write while using Obsidian. I don’t think that there is as much of a separation between the content a person makes and the way the tool influences how you create that content, as some tend to believe.
Even without using plugins this is a problem that everyone will have to face at some point. It’s great to have the open format, Markdown, but that’s not sufficient to prevent varying degrees of lock-in. In another thread, I was trying to raise this point by showing a screenshot of a very simplistic example of how different tools that support markdown but treat tags differently can change the way you structure your content. The example was probably overly basic but you can imagine, over time, changing your way of working to take advantage of tags in ways that are unique to the tool you’re using. This sort of feature/workflow lock-in is subtle and often doesn’t become apparent until you’re at that point where you’re forced to change for whatever reason.
Some people in this thread have recommended ways to mitigate the problem, which seems wise to consider. Still, I think it’s unlikely that it will be entirely possible to not be at least somewhat locked-in and experience some breakage.