A set neck is a glued-in neck, the old and proved method of attaching necks to bodies on stringed instruments. Set-neck versus bolt-on - well, in guitar terms that would be Les Paul versus Stratocaster. Alembic do set-necks and neck-throughs, and they build all the parts themselves (except the tuners).
The more affordable models like the Epic are built to the very same standards as the high-end models, the lower price reflects the use of less extravagant materials.
You needn't worry about truss rod adjustment issues, unless perhaps you use extremely light strings - even then, in most cases it can be helped with a heat treatment (or some time spent with a couple of phone books under the strings). The instruments are built to be adjustable, and many of the board members have found
Joey's Post on Setting Up Your Bass an excellent guide to do your own setup.
Like Taylor says, the standard Epic controls are vol, pan, bass and treble, so that should be a pretty familiar setup for most people who have played active instruments.
The signature Alembic controls include a low-pass filter with a Q switch, and no bass or treble controls. The filter offers a different approach to tone shaping, and requires some getting used to - but you will find tones that you cannot mimick with other instruments.
The Q switch is part of the low-pass filter, so if you find an Epic with a Q switch it was either ordered with a different electronics package, or a previous owner had replaced (upgraded) the electronics.
The Rogue controls include a filter and Q, plus quick-change toggles for treble and bass, which some might say is the best of both worlds.
Happy hunting!