How do you make sense of acid base reactions in organic chemistry? My question is in regards to acid base reaction that take place in larger chemical reaction in orgo. Like, I understand acid base reaction, how to qualitatively check which is stronger acid or base or where equilibrium lies, very well. But i feel that when I am trying to study the mechanism of series of other reaction like grignard mechanism, oxidation of alcohol, reaction with aldehydes etc… I see many intermediate acid base reaction in these mechanism that don’t make sense in terms of what I learned earlier when I was exclusively studying acid base reaction. 

For instance, I have seen many intermediate acid base reaction in larger reaction where an oxygen atom of one molecule attack H atom attached to oxygen atom in another molecule. And then I am thinking what the point of this reaction because equilibrium is gonna be in middle and not favor products since the conjugate base create will be acid right away anyways. 

Other times I have seen H20 act as an acid while molecule with sulfur atom act as a base. And again I am thinking how this is possible because isn’t sulfur a stronger acid then water. When I  asked two of my teacher about this. One of them said she actually made a mistake. But the main professor actually said that she is correct and to explain this, she said that water would even be hydronium ion here and when there is lot of water around, this water can serve as acid. However I couldn't fully understand what she meant by that? Can anyone please explain what she meant by this or how these acid base reaction possible. I have attached picture of what I am mean below to explain it my problem more clearly.
The answer to both questions lies in the fact that a reaction can be directed to a certain extent by controlling the concentration of the reagents.  The first reaction is perfectly fine since an alkoxide ion is more basic than a hydroxide ion. As for the second reaction, a carbon attached to an electronegative element is quite acidic. Hence is capable of possessing a negative charge. This along with the excess amount of water we supply for this reaction and the fact that water is neutral in nature adds to the reaction progressing in the forward direction. 

Hope this helps