I don't see why they wouldn't... considering they've done it when transitioning from 4S to 5. Unless I'm wrong on the implementation there. I don't want to sound like I know anything about how iOS renders for different resolutions, but I do genuinely want to learn.
Prior to the iPhone 4, all iPhone displays were 480x320 and that matched exactly the number of virtual "points" that developers designed around. When Apple doubled the vertical and horizontal pixel count of the iPhone 4 to 960x640, they kept the 480x320 points intact and simply had the iPhone 4 scale UI elements x2 so that a 1x1 point came out as exactly 2x2 pixels on the device and the device had 326ppi.
For the iPhone 5, Apple just increased the resolution to 1136x640 and the points to 568x320 -- this kept the scaling factor for the phone @ 2x again and maintained 326ppi. Legacy apps simply ran letterboxed until updated.
With iPhone 6 (4.7"), Apple increased the resolution to 1334x750 and increased the points to 667x375, and again kept the scaling factor @2x with 326ppi. Apps updated to take advantage of this point target will be able to display ~38% more content than 4" iPhones because of the point increase (667x375 vs. 568x320).
With the 6 Plus, the display resolution is 1920x1080, but the rendering resolution is actually 2208x1242. This came about because Apple wanted to be able to display more content on 6 Plus for obvious reasons, and thus needed a higher point count than 667x375. The number they settled on was 736x414, which ends up showing about 22% more content than the 4.7" iPhone 6 and 68% more than the 4" iPhones. With a 736x414 point count, Apple could have chosen @ 2x scaling, but it would have resulted in a 1472x828 display for a 5.5" phone -- far too low of a ppi. So they went up to @ 3x and had the phone render at 2208x1242.
Presumably 2208x1242 displays were too difficult for Apple's partners to make in sufficient quantity for the 6 Plus launch, so Apple used more readily available 1080p displays and has the phone render at 2208x1242 and then downscale by ~15% to hit 1080p.
Anyway, TL;DR -- because of the way iOS and its point system works, UI elements for the iPhone 6 Plus in standard mode *must* be 736x414. The only future alternative is for Apple to pick some other point target that scales evenly with 1080p, but that probably isn't feasible because it would result in UI elements that are either far too large or small depending on the point targets chosen. For instance, they could have chosen 960x540 and scaled @ 2x, but this would have made all of the UI elements tiny and unusable. 640x360 @ 3x is also an option, but this would have resulted in the 6 Plus displaying less content than the 4.7" phone, which obviously wouldn't work.
Edit: Apologies to any iOS developers if I misused the terminology (I'm an engineer, but in a different field) -- please correct me if there's an error with this explanation.