As someone who also uses SVN/Git repos and has written several build tools, I know where you're coming from.
Because of this, I have code that allows build tools to work off of relative paths. It's written in C++. However, the basic concepts are straightforward and the core algorithm (LCS) is available for Java.
Basically, you take the the full path of the export.json file as the root and the internal export path as a relative path, figure out the overlap, truncate the root to exclude the overlap and rebuild the path.
I'm using hashing to reduce the problem to longest common directories, and because of this the LCS algorithm I use is templated to work on integer arrays instead of strings. If you use strings directly, you'll probably have to fix the '/' tokens.
@[supprimé]
Worst case scenario is that you need to write a tool/script to open the export.json files yourself and repair the paths. In that event, what I would suggest is two .json files: one that lives in the repo with a relative path in the export settings and a second one generated from the first (by your custom tool/script) that is ignored in the repo.
You would need two tools: one to repair the export.json generated by Spine to truncate the path to the root of your trunk and the second tool to generate the user-specific json on the build system.
