It is also a lot of cable management if you want to work with a FX loop (4CM). The idea of having just one clean and complete pedalboard before the amp works fine for me.
For guitar it may be different because of the higher gain? Anyway this is a nice illustration from Andertons:
It is interesting that an extra EQ is in the loop. Nice way of controlling your effects.
Only time I use the FX loop is when I want to use a different (preamp) tone. The preamp pedal output is connected to the return of the amp so it skips the preamp of the amp.