You should be able to enter through a different port of entry but your residence application for the visa will restrict you from staying long enough.
According to a document on the Ministry of Internal Affairs Website,
Foreigners who would like to stay in Italy must apply for the
residence permit. Whoever arrives in Italy for the first time must
apply for the residence permit within 8 days.
One may argue that entering Italy is different from entering the Schengen Area. While this may be true, my situation while visiting France on a similar study visa prevented me from spending a long time outside France before my residence permit was issued/applied for.
As long as you can apply for the residence permit on time, while your permit is being processed, Italy allows you to travel in the Schengen Area for the first 90 days of the start of your visa. After that you can easily travel.
SINGLE ENTRY more than 90 days stay ITALIAN LONG-TERM STUDY VISA (type
D): With this visa, you can travel from Italy only within the Schengen
Area during the first 90 days of your visit; later, once you hold an
Italian permit of stay (see below) you will be able to travel freely.
MULTIPLE ENTRY more than 90 days stay ITALIAN LONG-TERM STUDY VISA
(type D): This visa permits you to travel in and out of Italy and the
other Schengen countries during the first 90 days of your visit; later
you will still be able to do it but only with a permit of stay (see
Unfortunately they do not explicitly mention whether you can enter the Schengen Area through another port of entry but since they do allow you to visit other countries for the first 90 days, I don't suspect any issues. Of course, the best way to solve this is to call VFS Global which offers Italian Visa services in India.