I think the 'classic' Alembic sound that your student was referring to is probably the bright, zingy, toppy sound that many of the more high-profile Alembic users use. I'm thinking primarily of guys like Stanley Clarke and Mark King, obviously - the guys whose names are attached to specific Alembic models - but there are others, too, who seem to favour the same toppy sound. The thing to bear in mind, though, is that these high-profile players are generally not typical 'supporting' bass players - they are the stars of whichever ensemble they may be playing in, often because of that bright sound, which enables them to take the part of a lead instrument to a greater or lesser extent, rather than the traditional supporting role of the bass.
We all know, though, that Alembics are capable of many more tones than those favoured by Stanley or Mark. And Jimmy Johnson's tone is a perfect example - he tends to play the more traditional supporting role (albeit with some wonderful flourishes here and there!) in the various groups he plays with, leaving the other guys, whether it's James Taylor or Allan Holdsworth or whoever, to bask in the spotlight. As such, he favours a tone which sits less obtrusively in the mix, and as a result, he's a less 'visible' bass player - i.e. while your average non-muso man-in-the-street may know of Stanley or Mark, he's unlikely to know Jimmy. So the overall perception of the sound of an Alembic is obviously going to be much more influenced by Stan or Mark's tone than by the hundreds of great, but generally less well-known players who choose to use Alembics in a less 'visible' manner.
If I were to try to define the 'classic' Alembic tone myself, I'd say my opinions of this have changed over the years. When I first came to Alembics, having grown up listening to Stan and Mark, I definitely thought the classic Alembic sound was that bright, nasal, toppy sound. But since acquiring my own SC deluxe, playing with the filters, and widening my musical horizons, from initially just playing with jazz-funk and fusion outfits, to now playing with a range of bands from country, to reggae, to metal, to ska, and getting to hear of some of the other great Alembic players out there like Jimmy, I've come to realise that, for me at least, the defining element of the Alembic sound is the extreme definition and articulation of each note, as opposed to the actual tone of the note. You can get everything from a zingy, toppy guitar-like sound down to a muted, rolled-off P-bass thump out of an Alembic, but you always get that articulation and definition at the beginning of the note, which responds to every nuance in the way you hit that note.
Fascinating discussion - I could go on for days, but I'm interested to hear what others think!