You do not need a "Preferred Fact" flag in the GEDCOM. Please read the following from the GEDCOM standard.
"The order in which GEDCOM lines are written to a GEDCOM file is controlled by the context and level number. When the lines are of equal level number but have a different tag name then the order is not significant. The occurrence of equal level numbers and equal tags within the same context imply that multiple opinions or multiple values of the data exist. The significance of the order in these cases is interpreted as the submitter's preference. The most preferred value being the first with the least preferred data listed in subsequent lines by order of decreasing preference. For example, a researcher who discovers conflicting evidence about a person's birth event would list the most credible information first and the least credible or least preferred items last."
If your software does not support this concept then it is not GEDCOM compliant and this should be reported as a BUG to the support line.