I tried compiling again but the import process in Godot fails and it gets stuck. By checking the code, it looks like it fails while unzipping the tpz file and opening the template, editor_node.cpp around this lines:
FileAccess *f = FileAccess::open(EditorSettings::get_singleton()->get_settings_path() + "/templates/" + file, FileAccess::WRITE);
ERR_CONTINUE(!f);
I made fat binaries, I checked permissions and that zip file was well generated with the right names when unzipped (I only replaced the necessary files) but it still fails. I thought this last part was the simplest but it looks like I am missing something in templates format (I even use .tpz extension).
I tried to place the templates in Application Support folder, but it looks like Godot 2.1.6 does not pick them from that folder (I have the ones I use with 3.2, so I made a folder for 2.1.6, and even tried to install regular templates but with no success, I cannot find where they are placed).
If I could manually place the templates where they should be, I believe it should work fine.