6S Plus has a very good CPU+GPU combo of A9 SOC. It also has 2 GB RAM. Both the SOC and RAM do compensate for the downscaling issues. The A9 is on the level of Core i3 Low power series. The GPU of A9 is even faster than those corresponding Intel chips.
But if Apple is determined to slow iOS 10 down, they can simply add few blurring or translucency effects and bam! Everything will be laggy and stuttery.
There is absolutely no guarantee whether it will slow down or perform same.
But given Apple's current track record, it will degrade in performance. How else will Apple market and sell iPhone 7?