I would expect it to be. Assuming they're like other V4 configurations, you now have two heads, intake/exhaust routing isn't as simple/straightforward, double the cams, etc. I would expect it to weigh more, take up more volume overall, and labor costs will increase as well. The list price of the new bike is high enough it could have still been profitable from a per-bike standpoint, but not as profitable as an inline. I think with Honda's shrinking sales in this segment they probably wanted to use a cheaper inline engine to make it a little more likely they'll recoup R&D costs. Maybe they also wanted to make sure people pay less for labor at the shop.
Whatever the case, they certainly know people want a v4 that doesn't cost a quarter-mil.
I wanted a v4 along with everyone else, but I would have been happy with some variable valve timing. I can tell VTEC doesn't have a great reputation for bikes, but the "kick" could certainly be smoothed out with cam profiles or electronic trickery. They would have been able to avoid a lot of the "gutless" complaints below 6-7k rpm. It's understandable why they didn't bother: reduced complexity, reduced cost, reduced weight, and because RACEBIKE who cares about low-end/mid-range power? Keep the revs high
Now I hope they don't release a V4 any time soon so that I can avoid having to explain to the wife why it's necessary.