I think that's a bit of a sweeping generalisation and I would be very surprised that even if that were true that it would be the reason for any difference in perceived audio quality differences. Firstly, we're comparing apples with oranges as 1. the transport protocols are very different, 2. The DAC chips will more than likely be different in any devices you're comparing and 3. The analogue output will almost certainly be different.
Any USB connected DAC is still going to be converting the incoming USB data to I2S. This is the common data interface when transporting audio data between local devices. It's robust and has separate timing and data lines, which is exactly what you want. USB connections are far more complex than a straight I2S connection on the Pi as you first have to convert your outgoing audio data to USB, then convert it back again to I2S once it hits the DAC. Far more opportunity for jitter to creep into the system via this method, but there will inevitably be some form of re-clocking going on which may help, or may hinder the results. My other concern with the Pi is that USB is shared over the same bus with Ethernet so if you're using both, there's bound to be some contention, even cross contamination of power here - I recently ran into this issue when testing different power supplies with Ethernet connected and the power supply to the Ethernet router was having a profound affect on the power supply to the Pi, which is when I switched to wi-fi.
I don't think there is a definitive statement when it comes to the Pi as to which is best. I2S connection is definitely the simplest, but then when it comes to the amount of space you've got to connect an I2S DAC, most of these will be limited as they will stick to the footprint of the Pi itself so as to fit neatly into a case. You can potentially do better with a USB DAC as it will be off-board, you're not limited in your board real estate and you can give it a dedicated power supply which can be isolated from the Pi entirely.
For me, I love the simplicity of the I2S interface and you have to go a long way to beat things like the IQAudio and Audiophonics boards. That's not to say that you can't get better by investing in a high end USB DAC though.