For ink (and inky) it is perfectly fine to mix absolute and relative paths when it comes to the includes.
I for example have something like this:
Master Ink File
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Assets/Game/Story/Master.ink
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INCLUDE Combat Chatter.ink
INCLUDE ../Levels/Singleplayer/001/001/Story/001.ink
INCLUDE ../Levels/Singleplayer/003/Story/Dialogues/003.ink
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INCLUDE ../Levels/Singleplayer/003/Story/Dialogues/01_village.ink
INCLUDE ../Levels/Singleplayer/003/Story/Dialogues/02_crossroads.ink