Due to the way this repository is structured, it is unlikely for users to directly fork it to create their presentation / Thesis / Proposal. Instead, users will copy the relevant sections, modify the license, and create a new repo entirely (such is the case here: https://github.com/leios/thesis).
Because of this, if there is a change in the relevant template, it is difficult to merge those changes to the working repositories. It is also difficult to make PR's because the working repo is not a direct fork of OIST/LaTeX-templates.
This is ultimately not a huge issue, but I am wondering if it might be better to split each template into its own repo (OIST/PhD-thesis, OIST/LaTeX-presentation, OIST/PhD-proposal, etc...) such that it's easier to pull changed from upstream or make PR's?
Admittedly, these are OIST templates and most OIST users do not actively use git or version control. As such, this is a really low-priority issue for now.