@Theroux I am unable to replicate that on my system. I tried it with multiple clips from different sources. Does this happen with every clip? More information about your video might help.
Also look to see that both your Audio and GPU drivers are updated - Especially GPU from the manufacturer (NVidia in this case). The GPU driver can sometimes affect the audio chipset since they are trying to stay in sync.
All drivers are up to date. Opening the file in VLC and slowing it there had no crackling. Changing just the pitch in HitFilm and not the speed had no crackling. Attached is a before-and-after sample (40% speed). Unless the crackling is somehow only on my end, it's pretty easy to hear.
@Theroux Just a guess, but it could be that the Shadowplay video is Variable Frame Rate? Might be worth a try to transcode it to Constant Frame Rate with Handbrake as a test. All my rate stretch tests were with CFR clips.
But everybody's system is different so who knows? My audio is an onboard mobo Realtek chipset and my GPU is an RTX 2070 Super. Just throwing that out as another data point.
BTW, I am unable to open the sample file due to permissions.