The equation of continuity is applicable only to narrow tubes of infinitesimally small cross-sectional area.
Consider a tube of above specifications. If the fluid(non-compressible) cannot come out of the side walls of the tube, it can flow in and out only through the cross-sectional area. In this limiting case of infinitesimally small cross-sectional area, we can consider the fluid to have a constant velocity. So, if we want to consider a tube of finite size, we would have to write $$\int \vec{v}_\mathrm{in}\cdot\mathrm{d}\vec{A}_\mathrm{in} = \int \vec{v}_\mathrm{out}\cdot\mathrm{d}\vec{A}_\mathrm{out}$$
Here, $\vec{v}_\rm{in}$ is the velocity of the fluid element going inside the tube and crossing the small area $\mathrm{d}\vec{A}_\mathrm{in}$. Similar notation is used for outgoing flow. So, in general, the value of $\vec{v}_\mathrm{out}$ or $\vec{v}_\rm{in}$ can change from place to place and can be at any angle to the considered area. $\mathrm{d}\vec{A}_\mathrm{in}$ and $\mathrm{d}\vec{A}_\mathrm{out}$ can be any areas bounded by the walls of the tube.
This result can be considered similar to Gauss' Law. If there are no sources or sinks inside the tube, the net incoming fluid flux should be equal to the net outgoing fluid flux.
Similarly, pressure also need not be same for every point of a cross-section. This can be verified by the fact that in a tube of finite size in which the fluid is at rest, the pressure at the bottom is more than up.