Apparently this is the behaviour intended by design.
Still, I think a hover condition should affect a conditionally formatted condition.
Yes, one for the suggestion box! improve the conditional formatting to include the 4 'states' of a object. (along with move conditional formatting to the Inspector)
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stumbled across this post, might be past due for a workaround but still.
duplicate the box you're using, have one with the conditional formatting & another with hover state, make the top one transparant (or both transparant)
you can fiddle with this technique to acquire the desired result.
I used this to have a list view with alternating grey fill on records and blue hover fill.
Rather than duplicate field technique as so well described by Maarten, I would rather use a single object (non field) and place conditional formatting on the object. Sometimes under a transparent field, sometimes as a "border" around a field (make the object larger than the field). These can work well without the field being on the layout twice.
A single space (box resized to fit needs) makes a very good "object" that takes conditional formatting.