It's patently obviously the intent is that everything below R-CG becomes R-CG. You've simply misconstrued the "base residential district" to mean "R-1", i.e. you read it to mean "Make R-1 become R-CG" whereas what it really means is "Make R-CG the lowest-density land-use district and everything below it go away".
FYI R-1 is the "base" district only in "Developing" neighbourhoods, and R-C1 is the "base" in "Developed" neighbourhoods. R-1 does not exist in the "Developed Area", and likewise R-C1 doesn't exist in the "Developing Area". In effect there are a set of land use zones for "old neighbourhoods" (R-C1, R-C1s, R-C1L, R-C1N, R-C2, R-CG) and a set for "new neighbourhoods" (R-1, R-1s, R-1N, R-2, R-2M), and R-1 is for the "new" while R-CG is for the "old". Obviously the City does not intent to replace the "new neighbourhood single-detached zone" with "old neighbourhood rowhouse infill zone".
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