While the calculations you've done are correct for an ideal structure, we are not dealing with an ideal structure here.
For one, you don't take into consideration the fact that the column is inclined. This will generate a static bending moment along the entire column, meaning you aren't dealing with buckling under compression, but under flexo-compression, which reduces the buckling load.
Also, your $L_{eff}$ assumes that the column is pinned on both ends. This is a conservative estimate, since there will be some rotational stiffness on both ends, but it's fine.
However, the biggest flaw in your calculation is that you assume that the buckling length of your "column" is equal to the height of the opening, but that is incorrect. The correct buckling length is probably more like the distance from the midpoint of the lid (where you sit) to the midpoint of the bracing beam near the ground. You then need to perform a buckling analysis for a column with a changing cross-section (from a solid section to a section with an opening to a solid section, with a changing width throughout). It this can be done analytically (no such guarantee), it will be a huge pain. This would be best done by letting a FEM program deal with it.
When modelling the column this way, the boundary conditions will probably be fixed at the base (due to the high stiffness caused by the tall bracing) and pinned at the top (the simple screw connection will offer little resistance to small rotations), which reduces your $L_{eff}$.
Also, as @Mr.P already mentioned in a comment beneath the OP, this calculation you've done is for Euler buckling, which is the theoretical limit for a perfect specimen. We are not dealing with perfect specimens in the real world, so designing anything by the Euler load is non-conservative (your actual structure will resist less than this load). In structures there are a multitude of codes which describe how to take imperfections into consideration, but I'm not sure if they are valid or practical for a small stool.
The best solution is probably as suggested by @alephzero in a comment beneath the OP: woodworking rules of thumb. I'm not a DIYer, so I don't know what these are, but I'm sure they exist and will give you a good notion of what's reasonable and what isn't. Also, there's no solution that's better than a prototype. Go ahead and build the stool. Sit (and stand) on it every which way, put some ridiculous weight on it (stacks and stacks of books and then sit on top of them), see how sturdy it is. Also make sure to test how "flexible" it is. A wobbly stool might not actually collapse, but the person sitting on it won't feel very safe on it.