My problem left me no peace, the more than there seems no one else to have it on the Kobo.
So I guessed that it might be my own fault, and, indeed, I found it!
I use KoboPatch, and among those, there is one called "Force user line-spacing in Kepubs". It overrides line-spacing set by the publisher in order to enable the slider of the device to take effect. This one I had selected, and therefore the issue. I removed it, and all's well!
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