However, thanks to allCountries.txt (in allCountries.zip), the coordinates for Europe are:
latitude = 48.69096
longitude = 9.14062
=> as a result, geotree uses data that are more precise than the ones from allCountries.txt, is it an error from geotree or data from allCountries are rounded at 5 digits after the comma?
The coordinates are stored as float in the database. In the extract files they are cut to 5 decimal fractions. This is an accuracy of around 1m which is more than enough for the features included in the database. Nothing is gained with adding arbitrary digits after the comma in the extract files, they don't add any information or value.