We used a custom company in Mass and the one thing I really liked was that you can specify any size cabinet you want. You can have an 26.75" drawer if you want. There are no filler pieces because everything is made to order. I was very happy with the cabinet construction.

Merrilat Claasic andTimberlake are at the lower end of semi custom so not the best reference point. If your finding local cabinets at the price of those your doing well.
Biggest concern is the finish-what are they using? A pre catalyzed varnish is ok, not as good as factory catalyzed but a sight better than urethane air dry.
Wood stability is a second thing to consider, ask about it
You will likely be finding pocket hole construction for frames. That would be the same as on the brands you mention. Moving up to the better semi custom brands you can start to find doweled frames, a big improvement.
As to custom sizes- there are a lot of semi custom brands that will do sizes in 1/8 inch increments. My entry level cabinet does.
One advantage with mfg cabs if your looking at line that do modifations and offer a good choice of accessories is engineering. I've seen a lot of odd approaches from local makers, course I've run into a few with mfgs but less often. And if there is a quirkie detail a brand uses the dealer should know enough to have you avoid it.
Bottom line is check the finish, see if it's domestic sheet goods, actually Blum AND price compare apples to apples knowing what the frame and box construction is. How do they attach the box to the frame?
A lot of folks on this board say they've gotten good deals. I don't know. What I do know is that when I built em, made everything, mortise and tenon frames, glued into dadoes and fastened- my prices were on a par with mfg brands, not much lower. Alas I had to use pre catalyzed varnish so to me they were better.
I could not compete with the semi custom brand I carry now even with the same (pocket hole) construction. Certainly not if I did not outsource doord and drawer boxes.
YMMV :)