If you use LaTeX for your thesis, then figure placement is handled by LaTeX automatically with some degree of freedom. I.e. you have limited control on where exactly LaTeX puts the figure. As LaTeX is widely used in academia, and it was created to produce well structured scientific texts, the outcome of LaTeX having its way, should be ok with your university.
I am not aware of any guidelines on the very issue you are asking about, so sorry for not answering your question. Official guidelines usally cover the style and placement of the figure caption, e.g. Table 3.3. has to be bold and that caption has to be above the actual table.
Generally, I would say the figure should be near the text passage which discusses the contents of the figure. As this is not always possible/feasible/sensible, I expect no hard rule to exist on this matter.
It is the standard behaviour of LaTeX with some document classes to flush all pending floating objects (figures, tables, etc.) before the next section/chapter. So, what you describe with Table 3.3. being the last item of Section 3.3.1 might be the standard set by the document class, it might also very well be by chance.
As for your first point, you can tell LaTeX to place a floating object not before the first reference to it.
Sorry for being very LaTeX centered, I haven't used Word much for scientific writing. When I used Word, I had non-floating figures, i.e. the placement was specified be me. Then my first rule for placing figures and tables was to make the paper "look nice", something that LaTeX does for you.