Is the default palette on startup hardcoded into synfig or can it be changed in a file somewhere?
As far as I know, the default palette is loaded at startup [1] and you can load a palette file that you previously saved.
But nothing (yet) like load a custom palette at startup.
The main “issue” with loading a custom palette at startup would where it will be stored.
In the main config folder for Synfig, inside a custom one, inside a project …
There are always drawbacks with such a feature, and it is not always portable.
Note that with AppImage v2 format, the portability of data is not a issue as you can have a folder xxx.AppImage.home or xxx.AppImage.config alongside with the AppImage itself
[1] Hardcoded in /synfig-studio/src/gui/modules/mod_palette/dock_paledit.cpp, in
Dock_PalEdit::set_default_palette()
Some apps stores a “default.pal” in a palette folder in user home directory (in the app folder in hidden folders > .config or .local on Linux). That palette file can be swaped or edited as its is a text (or css?) file.
I was just hoping Synfig had the same palette folder hidden somewhere…
It will come one day, it’s trivial to add as a feature, beginner friendly to code.
The thing is to define correctly the behaviour, for example, a revert to default palette could wipe your modifications if it is automatically saved as default palette 
Interesting request.
As @BobSynfig said, easy to implement. I’ll open an issue for new contributors.
Edited:
@Lae82 Please check if this is what you proposed: Let user set a default color palette · Issue #3773 · synfig/synfig · GitHub