Bob,
Maybe one of the easiest ways to remember what Water Based means is that, once the paint has dried, you can dissolve it again with water; as is often the case with certain interior house paints. I believe that people have confused what a particular paint cleans up as opposed to what it takes to dissolve it.
Having been in the automotive industry for some years, I may have another take on why a body/paint shop will not guarantee their paint when applied over another finish, including one that they may have sprayed themselves. What a customer hears and interprets is not necessarily what was conveyed or written on paper.
The paint shop says they will not guarantee their paint job when applied over another finish; the customer hears, they will not guarantee their paint job if the finish under the new paint job causes an issue with the new paint job, but the paint is guaranteed if an issue arises that, in the customers opinion, was the result of there being something wrong with the new paint or how it was applied. Ultimately, the paint shop just does not want the potential hassles this type of customer could present including being taken to small claims court. The shop may win the case but in the meantime they've lost time and money; even their reputation may suffer as a result. It does not matter if the shop was not at fault, if someone perceives the shop to be at fault...they are and they won't be bringing their car to that shop.
If it's possible to spray a waterborne paint over enamel, it may require sealing the old paint first...adds cost. I don't think or know if enough research has been done to determine the life of the waterborne paint under various conditions and applications. Were it my car, I would either strip the old paint or do as jcuprisi suggest; get your paint now. Strictly a personal preference...I always strip the car down to metal. My last Mustang had been repaired and I found Bondo as thick as an inch near the B-Pillar.
Ray