If you only want to perform MLM, then you don’t need to use BertForPreTraining, you only need BertForMaskedLM. The script is very easy to use as you only need to specify your text files and it runs!
In your case, this will look something like:
python run_mlm.py \
    --model_name_or_path nlpaueb/bert-base-greek-uncased-v1 \
    --train_file path_to_train_file \
    --validation_file path_to_validation_file \
    --do_train \
    --do_eval \
    --output_dir /tmp/test-mlm

Of course, a script is a bit like a blackbox in the sense that you don’t know the details about how training is happening exactly, but it’s much faster than writing a script or notebook yourself.