I gave it a try this morning with the latest master build of zephyr using the HCI_USB on an nrf52840_pca10059 dongle and I don’t get the errors/timeout issues as I save previously when I tested, however, GATT is unusable from bluetoothctl on linux (BlueZ 5.50). With the zephyr dongle, the device connects, seems to fail a connection parameter updates and disconnects – I am unable to list any details from the GATT server on the remote device (nothing comes through automatically and in the gatt menu, list-attributes seemingly does nothing). In comparison with a non-zephyr (cypress) based USB HCI dongle, it connects and instantly lists the GATT table, the connection parameter update still fails but even minutes later I am still connected to the remote device.
When I tested previously with a UART, it was with flow hardware control wired up to the FTDI chip. If zephyr was set to use it or not I cannot recall (it would have been the default for the HCI_UART example).