Perhaps my understanding is less in depth, but I've always seen it as a distinction on where and how the charges are levied: Art. 90 taxs take effect within the member state, Art.25 tariffs take place by virtue of the goods crossing a border.
See Van Gend en Loos for tariff prohibition under Art.12 (now 25), and contrast with Humblot and Commission v UK (beer v wine cases) for discriminatory internal taxation under Art.90.
The important thing to bear in mind when distinguishing here is "has the charge been levied purely because a good has crossed a border?" If yeay, use 25. If nay, but there is still discrimination, use 90.
Any hypothetical examples i could give would just be reiterations of the facts of humblot and commission v uk. Read the beer and wine case for the vital discussion of the difference between similar goods and goods in competition, and the different severity which restrictions breaching Art.90 on these will be dealt with.