That is a valid error message; means that the altName controlCR is used more than once in the Glyph Data loaded at startup. You can ignore it, just updating glyph names for a font that has a controlCR in it may yield an unexpected result.
I would be surprised if one console message makes a measurable difference in startup time.
I checked the GlyphData.xml file in /Applications/Glyphs.app/Contents/Frameworks/GlyphsCore.framework/Versions/A/Resources and it’s unedited (dated July 18th) and I don’t see redundancy/overlaps in the XML.
Also checked the application support folder and didn’t find any GlyphData.xml file there.
That’s it. There’s no other GlyphData in my filesystem. Attached is the XML file.
It could be a caching problem, or the routine getting executed more than once, file read twice into memory, etc…