It certainly seems odd to have a problem like this, but Essential has acknowledged and confirmed the issue via Twitter. The included cable is a USB 2.0 cable, and apparently causes issues when flashing or sideloading the device. The USB 2.0 cable is apparently intended to charge the device, not for anything else. It is recommended that you use a USB 3.0 device for flashing and sideloading.
Here's the tweet directly from Essential:
The tweet was just a confirmation to what they previously added to their beta build page. Essentials said it can result in an unusable device:
Don't use the cable provided with PH-1. Instead, use a USB 3.0 (or later) cable. Otherwise, it may result in an unusable device.
Equipped with this information, we recommend you follow their suggestion and use a modern USB 3.0 cable for any flashing of the device. It's rather odd to ship the device with a cable that the phone isn't capable of being managed properly with, but this may have not been an issue they were aware of beforehand. They do specify that you can use the cable for charging, as that's it's "intended purpose". If you only have the cable that ships in the box, definitely pick-up a USB 3.0 cable.