Hello, reporting in with the latest after applying the Sept 9 firmware update.
Short version: Although the Surface Pro 3 still consistently shows a lower link speed than my MacBook Pro, it now seems to be performing at a comparable speed when an actual file transfer is taking place.
Longer version:
As you can see in this photo (Mac on the left, Surface on the right, sitting next to each other), the MacBook Pro reports a link speed of 527 Mbps vs the Surface's 144 Mbps. Both are connected to the same 802.11ac network, broadcast on 2.4 GHz and 5 GHz using the same SSID from an Apple Airport Extreme.
First thing to note is that 144 Mbps is the highest link speed I've ever seen the Surface report in this configuration. Before the 9/9 firmware, I never saw it go above 72 Mbps.
Next, I proceeded to download a large (2 GB) file from my home server over my local network. After giving it a little while to settle, both computers reported a transfer speed of about 10 MB/s (megabytes, not megabits). This is also a notable improvement. Before the firmware update, the Surface would rarely achieve 2 MB/s.
So, although they still report very different link speeds, the actual throughput of a file transfer seems to have equalized between the two. At least, for now. This is good news, and is definitely new behavior since applying the 9/9 firmware update.
I will continue to keep an eye on it and report back if I notice anything else.