Why does FAR 27.409 say not to use FAR 52.227-19 for GSA Schedule Orders?

It’s because GSA has their own rules.  They have FAR deviations for software terms

https://www.acquisition.gov/gsam/part-552#GSAM_552_212_4

govt2310 said:

What is the rationale for this?

I might also add the same rationale that an agency would or would not used the clause as by my read the clause is not required.   The "may" in 27.409(g) along with  FAR 12.212 and 27.405-3.  Or in other words GSA has made a decision with regard to their GSA Schedules just as an agency would make a decision for any of its contracts.