Learn Dutch: Hij komt niet, maar zij komt wel. - He is not coming, but she is.

In Dutch, wel is often used as the exact opposite of niet (not). Because the first half says he is not coming (niet), the second half uses wel to strongly emphasize that she IS coming. It works like saying 'but she DOES' in English.

Why does the word order stay the normal subject-verb order after maar?

The word maar (but) is a connecting word that links two regular sentences together without changing their word order. So, you just start over with the standard subject-verb order: zij (she) followed by komt (comes).

Could I use the unstressed pronoun ze instead of zij here?

You could, but zij sounds much more natural. Because the sentence is making a strong, direct contrast between him and her, Dutch speakers use the emphasized pronouns hij and zij instead of the unstressed versions ie and ze.

The English translation says 'is coming', but doesn't komt just mean 'comes'?

Dutch doesn't use an '-ing' form the same way English does. The simple present tense verb komt translates to both 'comes' and 'is coming', and you can tell which one to use based on the context.