As I understand it, the port that USB is implemented on for the Pi machines is actually meant as an OTG port, made to act as a host by the drivers. On models with more than one USB port, there's a hub+ethernet chip. On the single-USB boards, they can actually be configured to act as OTG devices.
The whole situation means that OTG is unavailable on most models, models that have it only get one USB port (so OTG/host is an either-or proposition), and for the multi-USB+ethernet models, performance over those interfaces is worse than you'd expect (if I remember, BBB gets several times the transfer over USB and network, all at lower CPU usage, right?)
On the Pi 2, the ethernet port was really a USB-to-ethernet port plugged into a hidden USB port. So network speeds were limited to USB 2 speeds. I'm guessing the Pi 3 also works like this, instead of having pure onboard ethernet? But I don't know yet.
Given that USB 2.0 is 480Mb/s, and Ethernet is 100Mb/s, there is no bottleneck when using the Pi's Ethernet port. I really wish this myth that "Pi Ethernet is slower than dialup because USB" would just die.
Of course, like everyone else I'd love to see a new version of the Pi with Gigabit Ethernet directly connected to the system bus, and USB 3.0 while we're at it. But that would greatly increase the cost of the device and also require a newer SoC that supports such things.
I can't find any info to say which bus the MMC reader is connected to, but I know if you use a USB drive as well as the built in ethernet port, speed will suffer.
If it's using the same bcm2836 chip, then I think it'll have the same limitations. The markings on the chip in the pictures aren't quite legible enough to me, playing around in a photo editor, but it's marked the same way that the Pi2's chip is, from what I could see.