I've played the Ref Alto as my main alto for everything, particularly classical music for the last 5 or so years. It is a good horn, but I keep a wine cork in the bell to assist the bell notes and it's intonation is not a smooth curve. My horn has a wide interval between top C and C# for instance and these things have to be accommodated. The Ref Alto is more resistant and tends to have a more focused sound IMO. These factors, especially the trickiness of the extreme low register, plus the fact that it is a retrogressive approach the sound of the instrument, may have prevented your prof from recommending it.
The horns you list are all modern, forward looking horns: the S2 is a now considered to produce a 'traditional' classical sound but with more spread and better low register and general scale than older instruments and was designed to produce an inherently rather grainy sound (IMO). The S3 is purer and lighter in sound with greater freedom of response for a similar amount of resistance. Both are a serious commitment to learning their intonation but well worth the effort, both are full of personality in their sound and your choice really depends upon which sound you lean towards. The Yamaha is probably the easiest to become accustomed to, but also has it's peccadilloes; I found, for instance that with the G1 neck it tended to sharpness in the upper register (as does the S2) and that the bottom D was very flat, however the scale and security of the tone and pitch are very good. Some say that the sound of the Yamaha is blander than the Selmers', but IMO it's just different.
You should check out the websites of two SOTWers, SteveP who plays Yamahas, and drakesaxprof who plays Selmer S3s for fine demonstrations of how these horns sound in the hands of real pros. A sound clip is worth a thousand words!