Why at the bottom of the pipe of siphon pressure is 1 atm?
The pressure at the bottom of the right column is actually greater than $1\; \mathrm{atm}$, i.e., it is greater than the pressure at the surface of the bottom vessel, which is $1\; \mathrm{atm}$.
In other words, the pressure along the horizontal line $P_3$ is changing: from a higher pressure right under the column to a lower pressure at the surface. This is why the fluid is constantly moving. The pressure along this line would be constant, if the fluid was in balance or static, which, in an operating siphon, is not the case.
If we look at the whole picture, we could roughly say (without getting into details about various mechanisms involved in a siphon operation) that the fluid in the siphon moves due to the height difference between the left and the right columns, which introduces disbalance despite the equality of atmospheric pressure in both vessels.
Since, due to this disbalance, the fluid is moving, the distribution of pressure along its path cannot be determined based on the principles of hydrostatics.