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"High rise" cable guides are indeed a thing:
https://www.planetx.co.uk/i/q/FSPXMRBBCG/selcof-high-rise-underbb-cable-guide#FSPXMRBBCG
Some of the Planet X frames (London Road, etc.) use them.
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Hey took me a while but I finally got around to trying one of these and it worked perfectly, thanks for the suggestion! Moving the guide over did stop the cable rubbing on the chainstay but because of the position the cable was cutting inside which reduced the tyre clearance, which is now sorted with the high rise guide.
I've just cabled up the rear derailleur on this 1x build and the shifter cable is touching/rubbing the underside of the chain stay as it crosses over after exiting the cable guide (see pic). I've put a little patch of adhesive frame protector under there, but I guess it'll rub through that over time? Any suggestions on fixing this more properly? Shim under the cable guide maybe? Or are deeper cable guides which put the cable a bit further from the frame a thing?