The Sum is greater than the parts. This is what came to my mind when I was aggregating my PhD research into a thesis format in the summers. Thesis writing involves much more than compiling your research. It is analogous to not only writing a manuscript but also be the copy editor of the manuscript.
Firstly, the university rules and regulations have to be met. These rules can range from having a certain width in margins to font sizes and thesis organization. These rules can be consulted from the university examination handbook.
The compilation of PhD research also induces various major and minor consistency issues. There may be repetitions of concepts which need to be weeded out. In mathematical theses, consistency in notation is another issue. Maintaining macros is not only good practice but almost a necessity. In such cases, type-setting software like Latex is very handy.
Other aspects of the thesis such as preparing outline of the thesis, table of contents, list of figures, lift of tables and the index can take longer than expected and are not entirely trivial tasks. The bibliography is another aspect which needs to be taken care of. To makes the document, well-knit, references to definitions, sections and chapters within the thesis need to be input. Even if each chapter has conclusions, concluding comments of the whole thesis are expected in the end.
A thesis is much longer than a paper. Therefore, gentle reminders need to be inserted to remind the reader about certain terms defined much earlier.