> Presumably Manuka honey also inhibits beneficial bacteria in the 
> digestive system? 

This 1999 study: 

Manuka honey against Helicobacter pylori. 
McGovern-DPB; Abbas-SZ; Vivian-G; Dalton-HR 
Journal-of-the-Royal-Society-of-Medicine. 1999, 92: 8, 439; 1 ref. 

concluded that manuka honey is ineffective at eradicating H. pylori. Another 
unpublished NZ study found the same. 

So there is no evidence that it has any antibacterial activity once you eat it, 
i.e. unlikely to inhibit beneficial bacteria in the digestive system. 
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