This bug has to do with the default behavior of mlLoadSchemas and mlGenerateCode with regard to entity services (and given some time I'm willing to track down and fix).
If you use mlGenerate to create code from entity services, then it creates a TDE template and places it in
$configDir/ml-schemas
However, in order to deploy schemas, ml-gradle looks to
$configDir/ml-schemas/tde
The second location was a deliberate change, to provide a place just for extraction templates. So to fix this bug, my recommendation would be to change mlGenerateCode to save to the tde subdirectory.