None of what you described is specific to LaTeX.
In particular your third and fourth items (roman page numbering of the front material (then arabic for the main work) and index at the end) are the norm in many technical publications, not just theses. For instance a short list of books from the multitude that follow this ordering.
A.H.Wilson, A Theory of Metals, Cambridge University Press, 1936.
Jan Tschichold, The Form of the Book, Lund Humphries, 1991.
John Grossman (Managing Editor), The Chicago Manual of Style, 14th edition, University of Chicago Press, 1993.
Douglas Schenck and Peter Wilson, Information Modeling the EXPRESS Way, Oxford University Press, 1994.
Michael Mitchell and Susan Wightman, Book Typography --- A Designer's Manual, Libanus Press, 2005.
Note that the Cambridge University Book was published over 40 years before LaTeX was dreamt of.
Your other items regarding the position of captions and the style of bibliographic references vary from publisher to publisher and can be considered as stylistic as compared with the structural elements.
Your remarks about theses really have nothing to do with LaTeX but rather with traditional document structuring and detail. In any case LaTeX is concerned about typesetting a document and gives no constraints on the ordering of document elements (it will let you put an index before the title page if you wish).