Macs with a built-in screen are generally locked to 60Hz. Your Raspberry Pi is most likely also to be running at 60Hz.
The simplification applied by almost all emulators is to calculate an entire frame of the display, output that, calculate the entire next frame, output that, ad infinitum.
Therefore the software is pushing a complete new frame 50 times a second. Your Mac or Pi is pushing a new HDMI or composite image 60 times a second. Neither is doing anything in particular in regard of the difference. So you're probably not even getting as nice a conversion as a bad 24 to 25 — for C64 frames 1 2 3 4 5 6 7 8 9 10 you'll at best be getting output of 1 2 3 4 5 5 6 7 8 9 10 10. But because nowhere is it exactly written that 5 frames shall be output in 6 slots you also might be seeing some minor timing differences pushing one or the other frame backwards or forwards during the time that 50Hz and 60Hz end-of-frame timings are close.
On your Raspberry Pi, modify your config.txt for 50Hz if you haven't already. That should help a lot. Possibly you'll still get the odd frame that goes slightly askew because cross-platform libraries rarely tie neatly to platform-specific signals like retrace.
EDIT: with a little more research on the C64 specifically, one frame takes 19,656 cycles (312 lines of 63 cycles), but the machine is clocked at around 985,248.6111Hz (it's 17.734475Mhz divided by 18). So a real machine actually puts out about 50.13 frames per second. So even if you adjust the Pi to put out 50 that's still not quite the perfect rate. As you note though, VICE has an option to just lock itself to one frame of output = one frame of input. So then you're running your emulated C64 about 0.25% too slowly, but that should be a lot less worrying an imperfection than dodgy frame adaptation.
For comparison, quite a few 24fps movies are just sped up for PAL-region 25fps broadcast for the same reason. That's is a 4.2% speed up, so more than sixteen times as far off, but I've never met anybody who realised without being told.