I've finally had some time to look into this again. Things are starting to make sense with all your advice, but there is one hanging question that's in a way of everything - at least I think so.
Let's simplify stuff and focus only on the sample video with 500 Hz sound in the background (https://drive.google.com/open?...). When I drop it into Isadora and play it in a loop, what I hear is not only 500 Hz sound. At the end of each loop there is a delay/click. Is that only on my system, or is that a general behavior? If general, is there a way around it? Can it be codec-dependent, system-speed dependent, or what actually causes the 'click'?
Just to explain my reasoning - I realized that the deal-breaker now is the sound quality. In the examples above I just grabbed a guitar and played random chords to test things out in Isadora. For the show that I'm working on, the music will be recorded by musicians, and the click/delay in the loops is something I will have to deal with. It has to sound just right. I have an idea how to workaround the click using the Envelope Generator actor, but it's quite a convoluted solution that I'd like to avoid. I'd much rather find out why is there a click/delay between the loop in the first place.