I believe the aisle caps are bid for, and then arranged by, the manufacturers. The store just sells them the space.
The manufacturer is unlikely to see a problem with putting a display of very popular products right at the front of the store where people can't help but see it.
So you think Vanilla Inc, the company that only makes vanilla flavor ice cream, is paying for a whole chiller that they fill with vanilla, since all the other flavors are not as popular?
Or perhaps, unbeknownst to everyone in the world who uses the word 'vanilla' to mean 'mundane', vanilla ice cream actually enjoys far higher profit margins than all other ice cream.
No, I think Dreyers, the company that makes ice cream, uses the limited space available in the aisle cap to showcase one or two of their most popular flavors. (Or one or two flavors that are seasonally relevant.) That's a totally normal use of the aisle cap, just like how a Triscuits aisle cap is all original Triscuits and the many secondary flavors that Triscuits come in have to be found in the crackers aisle.
It would be literally impossible for an aisle cap to feature every ice cream flavor available - there are so many that each flavor would have very little representation in the display, and the concept would fall apart as soon as anyone bought something from it. At that point, you're paying a bunch of extra money to send the message "check out our least popular flavors".
It's unclear whether you're claiming 1. the vanilla ice cream is sometimes kept in a separate chiller must nearer the entrance and this obviously made-up story is perfectly true, 2. at least some stores exist where the vanilla ice cream (and only the vanilla) is kept in a separate chiller must nearer the entrance, or 3. the vanilla being kept by itself in a separate chiller has elements of plausibility, and can not be dismissed out of hand, even though it's possible that this specific set-up has never existed in any actual store in real life, ever. Which is it?
If you read my comments before deciding you needed to respond to them, it would be pretty apparent that I am claiming none of those things. I specifically noted that a refrigerated aisle cap is implausible.
What's not implausible is the idea that one flavor of a product with several flavors might be located far away from all the other flavors. That happens all the time.
The most popular flavors, by definition, benefit from advertising the most. The goal isn't to achieve equality of popularity between every product you sell. It's to sell the greatest number of products!
The advertising costs the same whether you advertise popular flavors or unpopular ones, but you'll get a lot more sales by advertising the popular ones.
Go check out a grocery store, see whether the aisle caps slant towards popular or unpopular product varieties.
The manufacturer is unlikely to see a problem with putting a display of very popular products right at the front of the store where people can't help but see it.