The Peptide Peak Found Ratio is the fraction of Transitions that have a good looking peak for that Peptide in that Replicate.
This is also the fraction of transitions that have a green dot next to them in the Targets tree.
The definition of "good looking peak" depends on whether the menu item "Settings > Integrate All" is checked.
When "Settings > Integrate All" is checked, a good-looking peak is any peak that is not completely flat.
When "Settings > Integrate All" is unchecked, the peak has to satisfy several more criteria including that the retention time of the apex be within 25% of a peak width of the apexes of the other transitions.
The Peptide Peak Found Ratio column is useful when you are refining an SRM method and are trying to decide which peptides are detectable and which transitions to monitor.
The column "RatioLightToHeavy" usually shows the same value as "Ratio to Standard", but that depends on exactly what you have selected for the Internal Standard Type at "Settings > Peptide Settings > Modifications". The RatioLightToHeavy column will show the ratio of sum of the peak areas for the light transitions divided by the sum of the peak areas for the heavy transitions. There is some information on how that is calculated here:
I will improve the tooltip for the "Peptide Peak Found Ratio" column so that it has more helpful information.