Currently, you can't use apertium installed in prefix1 to install a language pair prefix2.
If you, for example, installed apertium from the nightly apt repo, and you try to install a language pair from SVN, the modes will point at /usr/share (since that's where apertium was installed) instead of /usr/local/share where the language pair gets installed.
apertium-gen-modes should get the prefix as an argument and use that when creating installable modes.
Diff:
https://github.com/unhammer/apertium/commit/fe7652b87760b41bf09e8f34494b25310f515b84
Fixed in 68286