If you don't have enough light for proper exposure at the lens' maximum aperture and the selected shutter time and ISO, with most cameras the aperture indicator will flash to tell you the image will be underexposed.

Some cameras will also flash one of the exposure parameters if it thinks you've selected less than optimal exposure parameters. One example would be a camera that causes a selected shutter time of 1/15 second when using an 85mm lens - the camera is warning you that the shutter time might be too slow for that lens.

Your Sony camera may be warning you that the aperture value may be less than optimal for whatever reason. Are you using an exceptionally narrow aperture that might lead to diffraction? Are you using a very wide aperture setting that might lead to focusing issues with regard to the narrow depth of field being placed in the intended spot?

1/100 f4.5 iso 125 for example but its across all shutter speeds, apertures and ISOs when I attempt to replicate the values shown in the same situation using Intelligent Mode.....In shutter mode I can adjust all the settings to match intelligent mode and they don't flash but as soon as I half depress the shutter release the aperture indicator flashes....when I take the shot the exposure is as I wanted it....

What happens if you move the camera to point at a brighter or darker area than when you initially half pressed the shutter? Does the meter reading change, or stay in the same spot?

In Intelligent Mode the values keep changing if I move the camera with the shutter half depressed until I take the shot. In Shutter Mode with Shutter and ISO set the Aperture starts to flash when I half depress the shutter and does not change if I move the camera to a brighter or darker object.

Just took a shot in Shutter mode after half depressing the shutter then moving to a brighter object. The metering appears to have locked once I half depress the shutter. In Aperture Mode if I lock the aperture and ISO the metering is continuous...

Some cameras with certain settings applied lock in exposure upon completion of metering and hold it as long as the half press is held. Other settings (even with the same camera) will not lock in metering but will change it as the camera is pointed at areas of differing brightness. Your camera seems to be notifying you that exposure is locked, rather than continuous.