The short answer to your questions is yes, there is a way to set PicoScope to automatically save waveforms in the format that you specified, when using repeat trigger.
The buffer numbering is not limited to 32. It will go up to however many buffers have been used for the complete capture.
So, to capture 64 waveforms in 64 buffers, saved as 64 '.mat' files you need to make sure that there is enough buffer memory available in your PicoScope for 64 waveforms, when you are in Repeat Trigger mode. This will depend upon 4 things:
*The timebase you set
*The 'number of samples' you request
*The 'maximum number of waveforms' set for the 'waveform buffer'
*The size of the sample buffer in your PicoScope
You can increase the number of waveforms in the waveform buffer in Tools->Preferences (the absolute maximum being 10,000). Then you can either reduce the number of samples requested per waveform (the red circled text box in the image 'number of samples requested.png'), or change the timebase, or combine the two to reduce the actual number of samples used per waveform, and therefore increase the number waveforms captured (and saved to a file when you use alarms).
Using the setup shown in the image 'Alarms setup.png', and just the date for the file name will give you the file format that you want, if you are creating at least 1000 files (the number appended to the end of the file is sized according to the number of files that will be saved).