Based on your description of not having any Kobo-specific tags and the Kobo forgetting your chapter position in the KePub mode, you do not have a KePub at all but rather a standard ePub. It sounds like the Android app uses the same renderer for both, which is not the case for Kobo devices. Devices have the Adobe RMSDK for ePub files and the ACCESS renderer for KePub files.
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