From my experience birds don't seem to be concerned about the actual 'flash' component as much as the associated camera sounds, I have fired test flashes at birds and they don't seem to be alarmed or startled by it that I can see, but it's the click of the shutter at the same moment that gets the reaction sometimes if they are reasonably close. I think it's probably the racial memory of millions of years of being exposed to lightning out in the wild; a flash is a flash is a flash so to speak.
I sometimes use flash fill to try to lift the darker parts when the bird is in bright daylight, the differences here between the sunlit side and the shadow side can be large, the settings are basically expose for the bright side (ambient exposure, a quick an dirty method is to AEL the sky, but not white clouds) and set the flash to a variation of either full flash/ambient balance or – 1/3 or – 2/3rds. Any amount of flash fill greatly reduces the noise component in the darker sections of the subject.
If you are in an area of very low ambient and you want to capture a genuine realistic likeness of the subject colour wise and without noise, flash is a must, but you will have almost zero background detail, the shot will appear to have been taken at night in most cases….unless you can do some basic ambient/flash balancing that is, mainly juggling ISO will get ‘some’ ambient background into play and make the photo look more normal, flash will help greatly with noise control in the subject at high ISO but the background will most likely have plenty of noise. Myself I don’t really care if the oof background has lots of noise if the main subject is good, that’s the part that counts anyway. You will have to learn your camera, how the spot meter reacts and controls exposure so you have a feel for how the size of the target is going to influence the result etc. Also if the light level is low it’s probably quicker to MF than rely on AF as it can bring unacceptable delays in getting that shot, great shots can be missed because the AF went on an excursion right at the wrong moment.