Yes, this is an issue, but not, I think, a serious one.
The way I have approached this is to think of the primary categories as a hierarchy, something like retail → commercial → industrial → residential. These days there is little overlap of industrial/residential, but in town and city centres if the predominant ground floor usage is retail I’ll tag the landuse as retail, if office buildings at ground floor level, then commercial and so forth.
Thus an area like that around Langstrasse in Zurich, where there are shops (and dodgy nightclubs) on the ground floor and in basements, offices in higher levels of buildings and apartments in the attics, would be tagged retail. This makes sense if you think about what you observe in terms of movement and types of people in the area (footfall). You will also see this reflected in rental values for the ground floor sites, local authority zoning regulations etc.
In South-east Asia where the shop-house is a long-standing feature of even small towns it might be reasonable to use a different tag.
Once you have applied the main landuse tag there is plenty of scope for adding additional tags, such as residential=*. For instance I have used residential=student_village to distinguish residential landuse for gated sets of flats which can only be rented to students. Once could also imagine adding tags for secondary landuse (e.g., landuse=retail, secondary_landuse=residential), although I am unaware of such usage.
The key to these things is to ask what you want to use it for. We have established that OSM landuse has a good correspondence (both qualitatively and quantitatively, see http://sotm-eu.org/talk@38.html) with other landuse/landcover schemes such as CORINE and Urban Atlas of the European Environment Agency. Example applications of landuse/landcover include: hydrological models (using assumptions about runoff and surface sealing), ecological information (my own interest), resource utilisation, traffic demand models, etc. Within OSM we may well use landuse to determine if areas have been adequately mapped: landuse=retail with no shop=* nodes or ways points to missing data and so forth.
Lastly, the abutters=* tag is more or less in abeyance. It is a useful tag if you only pass through an area and cannot survey landuse. With the widespread availability of aerial images this is rarely a problem now.
HTH.