5.1k is a surprising resistor value, a lot of modern designs don't really have anything else in that area. I'm often not able to combine anything with it when I'm cost reducing. 4.7k, sure, but there aren't a lot of those either... 2.2k is just not close enough a lot of the time (or ends up as 1k), and same for 10k. So, sadly, it often does stand alone.
I wonder if PD will cause a comeback of that value as more and more legacy device refreshes move to USB-C plugs.
5.1k is about the middle of the generic "some kind of pullup" range of 1k-10k, so it's a perfectly fine option for strapping resistors or for a non-critical I2C bus.
4.7k would of course have been better because it's an E6 value (+-20 via the spec) rather than E24, but it's still a value I would expect any PCBA house to have in stock at all times.
But I agree, 1k or 10k would be the obvious no-brainer. I reckon there's probably a technical reason for it, as it does act as a voltage divider together with the Sink pullup, so perhaps there are some restrictions there with the multiple values it needs to distinguish.
Usually 5k is a little too weak for I²C. Rule of thumb is that you want to be around 1mA, so for a 3.3V system you start at 3.3k. Generally 1.8k to 3.3k ends up being a pretty common range. More current is usually better than less current, so even at 5V where 4.7k might be OK (if you're even at 5V Vdd these days), going stronger is often a good idea. If power savings is a concern, or if timing's somehow important (did you find another touchy badly behaved I²C device? say it isn't so!) then it might be time to break out the active pullup structures (mostly current source type things). Once this is done and tested it tends to get fossilized, for good reason, so this one won't usually get swept up in a standard-effort cost reduction pass.