Nice balanced review, and I agree with you on so many points. As you can see from my review (also on this forum) this is a car to love, and to niggle you at the same time.
Overall it's an excellent car in the most important aspects - driving. The arm rest is firm, and I can see how the centre console could 'get in the way' for certain seating positions - I have my seat quite far back, but upright and find that very comfortable over longer journeys.
Just use Apple CarPlay or Android Auto for sat nav - the only thing you'll lose is the directions in the drivers display panel.
As so very many have mentioned there are roof and general trim noises found the 10G Civic. Some can be resolved by yourself or your Honda dealer - some you will likely just have to live with.
Enjoy your Civic, I still don't think there's a car that matches it on it's strong points.