One of the major culprits in causing red channel clipping when photographing flowers in sunshine has not been mentioned in this thread, and that is WB. Sensors are most sensitive to green. Their response to light decreases as the wavelength decreases, which means they are naturally least sensitive to blue and would normally be most sensitive to red, however that high sensitivity to red means they are also highly affected by IR radiation. An anti-IR filter in front of the sensor also cuts into the exposure to red, which leaves green filtered sensels as the most exposed. Thus WB has a dual purpose; to boost the red and blue channels to parity with the green and then to further boost them to compensate for the color of the light. Daylight is blue so WB for daylight gives the bigger push to the red channel. Typically, it will more than double the red values and reds that were not clipped in the Raw capture will become clipped. The photo below,
has a Raw histogram like this:
The red channel has a maximum value of 7,399 (14 bit) but WB will increase that to above the clipping point (which for the Canon 5D2 is 14,736 after black subtraction). This is what will happen, for instance, with in-camera processing to jpg.
However, because the full, unclipped red data is there in the Raw, intelligent processing with LR will retain it. First of all, for a photo like this where most of the frame is occupied by the flower, the light that is entering the lens is not really natural daylight. It is daylight as reflected from the flower which has absorbed a lot of the blue component and is sending to the camera a much more reddish light. This means that daylight WB, in the range 5,000 to 5,500 is not really appropriate. I set it for around 4,000 and then tweak for the color I want. This has the benefit of reducing the amount of red boost (and increasing blue, but that doesn't bother me). Often this in itself will be enough to prevent clipping. If not, then the next step is to reduce Highlights and Exposure which globally reduces all three channels, of course, and then restoring the green and blue channels to taste.
A second problem, unique to LR but solved in LR4 with the inclusion of soft proofing, is that the LR histogram displays values relative to a very large gamut. Highlight values that seemed safely far from clipping might clip in a conversion to the small gamut of sRGB. For instance a value that might be 240 in a ProPhoto jpg will be 255, i.e. clipped, in sRGB. The use of soft proofing will predict this.