I hate the "what would Jobs have done" lines, but I think it is actually relevent here. Seriously. A man of Jobs vision and strength of will would have done something like this:
- Put in the higher spec CPU to give the 13" model the ability to have all four ports full speed. He would have made it part of his presentation as well, about the PCI lanes and how they were able to engineer 4 full speed lanes despite the challenges involved. He wouldn't have mentioned though that they were throttling the CPU in the 13" to a lower TDP due to heating issues in the smaller chassis as opposed to the 15" model...or...
Why don't we consider what Steve Jobs actually did? In 2010 he released a MacBook Pro with a Core 2 Duo processor, Thunderbolt, but only USB 2.0 while the rest of the market was releasing notebooks with Core i5/i7 processors and USB 3.0.
And if Apple actually did what you suggest by cramming a quad-core CPU and throttling it just so that they can provide full TB3 bandwidth to all 4 ports we'd have a thread with 1000 posts complaining that Apple has "lost it" because they are crippling CPUs.
The fact is that the "gimped" Thunderbolt 3 ports on the right still provide Thunderbolt 2 speeds and the charging benefits of Thunderbolt 3. Very few devices out there even support full Thunderbolt 3 speeds. Not many people are connecting RAID servers or external GPUs to a 13" notebook, and if they do, they can plug it in on the left side for maximum performance.