I agree with @dbl and @emartinezVic : both options are useful, but need perhaps clearer explanations.
continue : take all from the saved model, most parameters can be changed on the command line, like epochs, learning rate, fixed embeddings, ..
train_from : take all from the command line, not-specified parameters are the ONMT default ones not the model saved values (except for few mandatory ones, of course, like the net size or the embeddings).
In my own current experiments, being not really sure of what is doing the "continue" option, I'm always using the "train_from" option. What is really lacking in such usage cases : a full report of all used parameters values on the log file at start ! It's the only way one can be sure of values ONMT is using when running. This full report can also be an option.