If you have an ideal CRT and don't want to adjust where the electron bean lands, you don't lost any energy in #2 and #3. You can replace #2 and #3 with some perfectly isolated plates with a fixed amount of charge that have the same charge forever.

If initially the position of the beam is in the center of the path , a charged #2 and #3 will change the direction and in a smaller amount the velocity of the electrons. The energy to change the velocity comes from the energy in the electric field, not from the plates.

You can say that this energy is energy of the electric field or that it is potential energy of the electrons in the electron beam. Both descriptions are accurate and give the same result. Just remember to not count it twice.

Now the question is where does the energy from the field or the potential energy of the electrons came from. The answer is that the repulsion has a small but not 0 effect outside the main part of the capacitor and this creates an electric field outside. To align the beam at the center you must overcome this small force, so you must add some energy to the electron (in this case it's easy to think in the potential energy of the electron). Perhaps the comment from ballenarosada is more clear https://news.ycombinator.com/item?id=17432975

In a normal CRT the electron bean is created from a high voltage source so it moves fast, and the electrons initially move inside wires, so you usually ignore the small potential field of the capacitor far away. If the charges move slowly and freely then you must consider the effect of the electric field outside the capacitor.