The Mughals at this point haven't arisen yet. Would they actually try to take over the spice trade though?
I don't really see why they would, what they could aim for would be a monopole of production (I don't know enough of Mughal history to say if it's likely or not, even if my impression is there wouldn't be something that pushed off), but what mattered of Mameluks was the control of spice trade up to North Africa and Europe.
Portugal's collapse would certainly have removed a potential rival in the New World, with Spain actually taking Portuguese South America. I'm not sure if they would have the time and resources to conquer India, given the need to administer their new conquests.
Thing is, Spain without Portugal on its way would probably just take its place. Their aim was the very same than theirs, they just tried to get around Portuguese maritime domination by new roads.
It's quite likely that Spanish traders and sailors will do the junction with India eventually, rather than trying to go by West (being seen as a foolish move originally, and quite truthfully considering Colombus' assumptions on Earth's size).
Discovery of America is still gonna happen sooner or later, and probably with at least tentatives of conquests similar to IOTL.
It doesn't mean Indian spice trade takeover is going to take the same roads, and Portugal absence would most probably delay the Mameluk loss of their monopole, giving them more time and as well Mughal presence you mentioned to limit TTL effects of it (without probably butterflying them as such).
Critically without Ottomans, it means that Spain have a free-hand on Morroco and Algerian's coast (more than the IOTL conquered harbours by Portugal and Spain), that they won't have to deal with two rivals for maritime domination, and that spice trade is going to fuel other conquests.
When it comes to parallel PodS : unless using a more earlier one, probably with Il-Khanate crushing the hell out of Ottomans and Turkish advances in Balkans, somewhat going into a much much weaker Spain and Portugal at the same time thanks to butterfly effect... It's going to be hard, and more you go begin early, more it's going to be unreckognizable and hard to predict.
I think you'll better off with only one of these getting rid of, and Ottomans absence seems more likely to me with the latest PoD avaible (that said, this last consideration is only a favourite of mine). Savafids are going to be a pain, and loss of Syria/Arabia quite possible (while less problematic) but Mameluks may live on.