VisualEditor is not the only consumer of the Parsoid styles. Flow needs them as well.
The solution is to move the general Parsoid styles from VisualEditorOverlay.less to Minerva's version of the 'mediawiki.skinning.content.parsoid' module.
You should consider whether you really want to maintain an entire fork of this module. A better solution may be to keep general-purpose styles in the 'mediawiki.skinning.content.parsoid' default module (which already exists in core), and move ones you consider too Vectorish into Vector's skinStyles, using the '+' option (see $wgResourceModuleSkinStyles).
Regardless of which approach you take, it needs to have feature parity (see e.g. T93856: an inline external link in square brackets without a title doesn't appear in Flow pages on mobile web).