Disclaimer: I'm not a lawyer. I just did some research for my own library (by reading and looking at other repositories) and noticed that there are some problems with your LICENSE.md file and your license headers:
I just wanted to let you know as I think that it's relevant for you. It's up to you, what you make with this information. Personally I came to the conclusion to not add any license headers to any of my files as they are not required by law (see https://ben.balter.com/2015/06/03/copyright-notices-for-websites-and-open-source-projects/). If you decide to keep the license headers, I would recommend the wording from my linked article:
Copyright [year project started] - [current year], [project founder] and the [project name] contributors.
To your first point:
The template is part of the APPENDIX, which can be seen as part of the license or not. In the case of seeing it as part of the license itself, you would argue that the license is derivative. This means it is technically acceptable to alter the template in this case. I do think it is strange to alter this template myself so I will update it either way.
On your second point:
You do mention the GitHub ToS here which speaks of rights belonging to contributors. This means the right agreed upon can be invoked and thus allows contributors to alter the license and add their own name. If that does not happen in their changes it is valid as invoking and using this right is not mandatory.
Despite all this, it is common practice in the industry to apply this header to files with only the project copyright holders being mentioned. As this is common practice I don't believe we need to worry about it in any case. I am willing to speak to a lawyer if it comes to this but I don't believe we break any rules here.
To follow up my reply to the first point:
According to the license agreement the appendix is not part of the license and thus can be altered.
"License" shall mean the terms and conditions for use, reproduction,
and distribution as defined by Sections 1 through 9 of this document.
This means it can be changed or even removed from the LICENSE file.
Additionally, @DV8FromTheWorld does not want to change how we alter the template and I don't want to go forward with changes we do not agree on, especially when it comes to licensing.
@Bastian thank you for thinking of us but it looks like no changes need to be made in our case here.
Like I said, it's up to you what you do with this information. I don't really care, as I'm not even a contributor.
As my last reply to this issues, I just want to quickly comment the second point with a quote from one of my links (https://ben.balter.com/2015/06/03/copyright-notices-for-websites-and-open-source-projects/, the last sentence of the "The founder-contributor distinction" part):
In either case, just putting the project founder or maintainer is strictly speaking wrong, assuming others have contributed.
I'm not aware that it's common practice to omit some copyright holders, but you are most likely correct that this will not have any consequences ever. This doesn't mean that it's correct though.
I believe this PR should alleviate that: https://github.com/DV8FromTheWorld/JDA/pull/885