The use of Bernoulli's equation with a siphon and similar problems?

There are a variety of problems in fluid mechanics that involve the flow out off, for example, a beaker. A typical example is that of a siphon shown below:

(From wikipedia, by Tomia, CC BY 2.5)

The typical way to approach such a problem is to use Bernoulli's equation at the top of one of the beakers and e.g. within the tube. I am yet to find a satisfactory justification for its use in such a situation. I guess we are not assuming the flow is irrotational. In which case a streamline must connect the points of consideration which seems unlikely. So what is the resolution to this i.e. why can we use Bernoulli's equation in problems such as this one?

• The Bernouill differential equation? en.wikipedia.org/wiki/Bernoulli_differential_equation This is a mathematical form of equation for which it is easy to find solutions. You have to use something else to define the physical laws of the system to get the equation you want to solve, in order to then apply Bernoulli to actually solve it. If you want to know flow rate you can resolve newtonian forces due to gravity in the siphon acting acros it's cross-sectional area to get the equation. – JMLCarter Dec 26 '16 at 22:15
• @JMLCarter No I am talking about the equation given in en.wikipedia.org/wiki/… – Quantum spaghettification Dec 27 '16 at 10:32
• back to square 1, then, (find time to re-interpret the question :-( – JMLCarter Dec 27 '16 at 21:58