As a rule, yes, but not necessarily and not everywhere. The important part is to have a coherent set of units, which usually is going to be SI units, but not always. If the user's preferred unit never is going to be SI, does it make sense to base your program on SI units?
For example, aviation deals heavily in flight levels (multiples of 100 ft). If flight levels are a first-class concept in your program, then you're already using non-SI units below the presentation layer. At this point you've established that some altitudes in your program are expressed in feet, and it might be a better idea to use feet for altitudes everywhere rather than introducing a lot of unit conversions. Or it might not be.
I took it as in the presentation layer, but I can see where you're coming from. In that case I would agree with you, and I'm not sure why GP would complain about that.