La chiesa di Sant'Antonio Abate was my family's church prior to our emigration to the USA. It is a beautiful church and is considered a jewel of the baroque period. It was built circa 1572 and remains in its original state. It offers gold-gilded altars and ceiling by my 8GGU Giuseppe Petti of Oratino. Giuseppe and his brother, my 8GGF Gioacchino Petti, provided gold-gilding for many of the churches of the region. It also offers a wooden statue of San Francesco by my 1C9R Paulo Saverio di Zinno.
At the time of its construction, Sant'Antonio Abate was the "new" church in town, the first built outside of the medieval walls of the town. It was not the mother church, having been preceded by San Giorgio (the oldest church, circa 9th century), San Bartolomeo, Santa Maria del Monte (originally Santa Maria de Supra), San Leonardo, Santa Maria della Croce, San Nicola, San Paulo, Santa Maria Maggiore (la Cattedrale), Sant'Angelo, and San Mercurio (later combined with Sant'Angelo). For those of you from Campobasso or the surrounding area, a tour of the churches of Campobasso is very worthwhile. However, you need an appointment to see San Giorgio and San Bartolomeo, which are now closed to the public. Furthermore, Sant'Angelo is no longer in existence (once located just below Castello Monforte), San Nicola is now an office building, and San Paulo and San Mercurio appear to be abandoned.
By the time Sant'Antonio Abate was built, la Cattedrale was already considered the mother church and the ecclesiastical records, beginning in 1568, support this. If your grandmother was born in the comune of Campobasso, this is where you would find her baptismal record. If she was born elsewhere in the province of Campobasso, then you have to identify the town of birth in order to locate the record.
PS: I read your post as meaning "mother church" as a relationship to other churches or an area. If you actually mean "Mother Church" as a name or title, then I'm afraid I may have confused the issue. If so, I apologize.