External mixers:
The are less expensive than mixer modules.
They offer more features.
They don't eat up HP space.
Internal mixers:
Operate at synth level.
Can offer CV controllable features like pan, volume, etc.
Fit conveniently in your case.
If you're using an external mixer, you output synth levels from your case into line level inputs. Some mixers can handle it... others can't. You may need some sort of synth-to-line-level converters. If you pass an output from the mixer back to Eurorack, the volume levels will be a lot lower and you'll have to boost the signal somewhere (which can introduce problems with noise-floor, etc.). If you want to use a Eurorack effects unit from an external mixer's aux output... you'll see what I mean.
Eurorack mixers are bloody expensive with only a handful of channels and they take up a lot of HP. If you're lucky they might have EQ and maybe one or two aux sends but usually not.
So it comes down to needs, knowledge, and budget. Each approach offers pros and cons and there really isn't a "best practice" model out there. You just have to pick your poison.