The recent proliferation of Indy chukkas to be is clearly a way to get around other exclusive makeups. Other people have locks on all the Color 8 antique edge Indy variations? Then we'll do ours slightly shorter, and bam, you're in the ballpark of your desired shoe. I think this will continue to be a trend as the Alden world expands.
I'm trying to adjust to them too. That said, depending on how you wear them, they probably can be roughly equivalent- you have to work to show the tops of your boots anyway.
I don't believe any Alden is truly exclusive to any retailer.
I think the chukka style looks better with a plain toe. When I see the indy stitching, I expect to see a high boot with long laces wrapped around the ankle. I also feel like I get more for my money with the longer shaft. Cordovan ain't cheap.