Take this with a huge grain of salt, but this is how I interpret the word:
Many people like to imagine the universe as operating a lot like a computer program, a simulation involving rules, and calculating future states based on those rules. Now, I'm not here to argue that that's the "correct" way to view the universe, but I am here to say that if you're at all inclined to accept that that could at least be analogous to how the universe operates, then here's what "fundamental" might mean in such a context:
If the universe is a computer program simulation, then the things which are 'fundamental' in that simulation are the things which have either direct, strong referents, or at least indirect but obviously implied referents, in the source code itself.
So, the "universe" of conway's game of life has, as a fundamental entity, a "cell" or "pixel". Those cells are strongly referenced in the source code, and the source code calculates the future of the Conway's universe by operating on those cells.
Gliders, while being an immediate consequence, aren't purely fundamental because they aren't referenced in the source code - however, they're so close to being fundamental that it wouldn't be surprising if an intelligent being who lived in Conway's universe discovered them and thought they were fundamental.
When someone says something isn't fundamental, to me that means that it's not at the lowest level of reality, it's not a building block of reality that's strongly referenced in the source code - instead, that thing is the consequence of the source code running.