I found a solution: we can cut off selected output data of the id_data object before using compare:
compare(id_data(:,50:70,:), model)
This will now only plot output channels 50 to 70, but will also produce some warnings (one for each missing output):
Warning: Output channels required for prediction or initial condition estimation are not available in the validation data object. Prediction horizon of Inf and zero initial conditions will be used.
These warnings can be suppressed via:
warn_id = 'Ident:analysis:compareChk16';
warning('off',warn_id)