Morning Andy
Just catching up...
The mismatched grain irritated me too, but I'd only seen it in the cabin foot well sides, some vertical and some horizontal grain. Not really seen, so not a big problem, pity they've done same where it matters on the deck.
Re the stern ply to plank issue. If the trim can cover, that's got to be best option as it's least risk I'd have thought. Another approach would be to use some ply offcut and set it into the problem area, and blend it... Big risk though as that ply can't take much blending or the light ply layer is exposed.
Not sure about that forward to side deck join either as I'm not at that point. I'd look at dry fitting the remaining parts in that area and see if it gets covered, whether it matters...
Best regards
David.