As someone who has run a business in which labor was my biggest cost, I can say that it's the little things that can add up. I was always looking for places where we could save time on things that didn't matter, so we could invest more time on the parts of the job that really do.
I remember meeting some of my former guys who had gone into business for themselves, who used to gripe about how I focused on so many details that made guys more productive, tell me that once they had their own business, they now understood.
Plus, you never look at one particular job. Just because I hit a grand slam on an easy job, and made a lot of money, (or more correctly, knew I would as soon as I got the job) didn't mean I could do things differently on that job, because there'd be another one in which I may only make wages, and no profit. So I can see a guitar company being concerned about where they can save costs, even if it's on a more profitable guitar, in order to help make the models with tighter margins, also be profitable.
Employee labor in the US is a business cost you have to stay on top of every step of the way. I couldn't imagine trying to attract people for an entry-level job that probably pays not much above minimum wage, doing what I consider the very boring, repetitive task of hand sanding.
And personally, I couldn't care less that the back plates aren't recessed on my EBMM guitars. I'd rather they spend that money on something more important anyway.