If you use the dtoverlay line in config.sys as per mikerr a BT dongle still works fine. That is how I am running.
Daily driver: Pi3B, 64GB Samsung Evo+ @100MHz, DVB-T, onboard WiFi for internet, BT/USB dongle for KB/mouse, 250GB HDD via USB for media, Raspbian Jessie Lite with Openbox desktop. Museum: Pi B