I can confirm the audio crackle. Since disabling HW accel decoding reverses the crackle (tested by you, I did not verify), that points to something in the gbm_matrix branch by popcornmix as causing it. Recommend you open a post on the
kodi forum mentioning that you are using popcornmix's gbm_matrix branch and use the @popcornmix tag in your post so he gets a ping.