Not a chance. Portugal's insistence on converting people--and inability to dominate the Mughals in their prime--would have been only the first major roadblock to their domination of all of India.
They also had that union with Spain--an unmitigated disaster for Portugal--European competition running "better" stock company models, and a lack of manpower.
Britain managed to dominate India because the French lost against them, and because they arrived on the scene just as the Mughal Empire began to slowly decay. This allowed them to manipulate internal politics, through the BEIC, to gain land and economic privileges, allowing the BEIC to field more armies.
This. The British entry into the Indian political scene was literally at a time when Northern India was continuously in a state of devastation where the Mughal Empire was losing its power. It was a very particular series of events where the Company was able to assert its authority; and they had the added benefit of surviving a disastrous war earlier on from 1686-1690 where they were allowed to keep their land.
One also has to remember that the British paramountcy was established by working within the system of legitimacy in Mughal India. Until 1858, the East India Company was a legal vassal of the Emperor in Delhi, and ruled the subcontinent in his name. Their expansion in India was conducted under this legal reality as legitimacy was a very important part of the British adventure in India.
The conquest of India boils down to the deterioration of an old Empire; a lucky conflict between nobles in an important province of said empire allowing the British to intercede; working with a lot of local support from bankers and brokers to nobles, and convincing Parliament that the Empire in India was a worthy endeavour (there was quite a bit of opposition); convincing the Emperor to grant them revenue rights while he had escaped the Qila- Mualla to the confines of Allahabad in British influenced territory and being able to engineer a coup to consolidate their administration since the rest of the Empire was so busy fighting off the other threats that were at their doorstep.
I just can't see this combination of fortune and wiliness happening again to enable the Portuguese to go through the same thing.