Last week I was able to compare the HR-V and Civic in detail, because they were lined up next to each other. Next to the obvious differences (Civic being much lower and sportier; mind it was also the 'Sport' version, HR-V more roomy and higher, lighter in color) I also noticed that the HR-V is much more luxurious and has better materials used for the interior. The Civic, all black, partial leather seats, felt much less refined then the HR-V.
So I can imagine the HR-V costs more in terms of interior and the Civic in terms of drive train. If I had to choose - and you would have asked me that question 2 weeks ago - I would have said Civic without any doubt. But now, I think the HR-V would actually be my choice. It made a much more positive impression than the Civic. I haven't driven either, so that's still on my to-do-list.