I've read some of those web articles about this topic, and they note other beers, especially the porter, made the trip, but they never give the recipes of these other beers! It's just a fact that they put up with spoiled batches of beer back then, so I don't think we can say that wasn't a major concern. And spoiled rations or goods were an even bigger concern on long ship journeys back then as well. In one extreme case Magellan's water is said to have rotted as they were going across the Pacific. It just seems unreasonable to assume that they didn't worry about spoilage or find methods to reduce spoilage.
So it definitely makes sense that they would seek out a way to reduce spoilage on long sea journeys scientifically speaking. Perhaps they didn't brew IPAs stronger, but definitely hoppier, and we know that hoppier beer is less inclined to spoil.
It is an interesting idea that they may have watered it down after they arrived. Or maybe that it was meant to be watered down at least, it would have to be done right before drinking, because splitting the IPA with a barrel of water would be a sure way to make sure it went rotten after a few weeks. If the guys stationed in India thought it lessened the quality though, the practice wouldn't necessarily survive when they didn't have to do it.