I understand that you want to handle the issue of logging and comparing data from a continuous system and a triggered subsystem in Simulink.
In the Simulink model configuration parameters, under the "Data Import/Export" section, you can specify the logging options. You can adjust 'Decimation' and 'Logging intervals' to control the rate and intervals at which data is logged. When you only want to save and analyse data for particular time intervals, you can specify the time intervals in which to log data. Using logging intervals allows you to save specific data without changing or adding complexity to your model.
If you want to log a signal from a triggered subsystem at a fixed rate, you can use a Rate Transition block to resample the signal to the desired rate. This block can help you to bridge the gap between different sample times.
For further information, refer to the documentation links below: