In general, MATLAB cannot handle interrupts and timers. There are ways of using interrupts using Data Acquisition Toolbox
as seen here.
With audio samples in the hard drive, you will not be able to make use of interrupts. MATLAB does not allow you to pipeline the tasks. MATLAB allow does not allow the user to multithread, because bad things can happen. Instead, some of the operations in MATLAB are multithreaded and you get to use in your program. That said, you could finish processing with method 1, get data, and then switch to processing with method 2.
Sample by sample data processing is available in MATLAB. But with audio samples, it is better to use a window.