It's wholly intentional, of the bean-counter intent; Mesa set it up this way for the same reason it ships ALL its tube amps with the tubes biased VERY cold, to minimize warranty claims both on the tubes and the amps. You could pull half the tubes from a 400+ and if the amp were set up for full power and easily get the same amount of power (about 180 watts) that one with a full tube complement factory stock puts out. They're good amps, but people should be aware of their characteristics, which Mesa doesn't like to trumpet. If you read Bass Gear magazine, all you need to do is look at the frequency response plot published in the latest issue of the Prodigy and Strategy amps to see that they also have this inherent low end rolloff. Fender didn't do it in the designs that ALL of Mesa's amps come from, but Fender also had a much better supply of power tubes of higher quality.
It's not a "tube amp thing" either. I have seen few self proclaimed experts chiming in on TB that low end rolloff is part of using an output transformer ...except low frequencies are the easiest thing for them to pass until you get below 10Hz, and no speaker is going to be hitting that, nor any instrument putting it out anyway. (Highs above about 2-5kHz require complex interleaving of the OT windings so that the transformer's own inductance doesn't muffle and roll them off, but that's another topic).
My current go-to amp is my Mesa 400+ and while it isn't quite the monster that some of my others are, I feel that I've finally got it to sound and perform the way I like, so I'm not dogging Mesa. I love that little bugger and it's a nice living room compromise between my B-15 and SVT and bigger tube amps. I just have to keep that 40Hz slider on the graphic EQ pretty much near full boost just to make the amp be honest about what it puts out. I do love the odd midrange character the amp has, and it's not hard to hear Cliff Burton's tone (what was audible anyway) in the 400+, which was the second generation of the amps he played in Metallica, early D-180's and Bass 400's. That low end rolloff may have been what inspired him to put that mudbucker in the neck position of his Rick 4001.